sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7d315502780691220bf3b9e86d544caeddd56a3ef0edf82072e144197f3faba6 | C/C++ | 662 | 22 | #ifndef CODE_Quantifications
#define CODE_Quantifications
#include "IncludeDefine.h"
#define uintQ unsigned long
class Quantifications {
public:
struct {//counting reads per gene, similar to HTseq
uint32 nGe; //number of genes
int nType; //number of count types (columns)
... |
966eb9cc9b166a598e4c0853ea8ec07b6cbb438e75d5582485fc2982593d29c6 | C/C++ | 676 | 29 | #ifndef THREAD_CONTROL_DEF
#define THREAD_CONTROL_DEF
#include "ReadAlignChunk.h"
#include <pthread.h>
#define MAX_chunkOutBAMposition 100000
class ThreadControl {
public:
bool threadBool;
pthread_t *threadArray;
pthread_mutex_t mutexInRead, mutexOutSAM, mutexOutBAM1, mutexOutChimSAM, mutexOutChimJuncti... |
5490008f2669ff1502cf7715cee2dbbf5742733872e0a30f96db3951a2d4ba8a | C/C++ | 683 | 36 | #pragma once
#ifndef INDENTATION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define INDENTATION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "ostream.h"
#include <iostream>
namespace YAML
{
struct Indentation {
Indentation(unsigned n_): n(n_) {}
unsigned n;
};
inline ostream& operator << (ostream& out, cons... |
6f82c52279e8f79165f4446be652e5741a49992ac58632470335aa34c564072a | C/C++ | 708 | 37 | /*
Additional tools for Minizip
Code: Xavier Roche '2004
License: Same as ZLIB (www.gzip.org)
*/
#ifndef _zip_tools_H
#define _zip_tools_H
#ifdef __cplusplus
extern "C" {
#endif
#ifndef _ZLIB_H
#include "zlib.h"
#endif
#include "unzip.h"
/* Repair a ZIP file (missing central directory)
file: file to recov... |
d7a2922315abc3ccf4cb5a4fc3ba3366238aad40838da04ce8dec3e9a5f86471 | C/C++ | 716 | 30 | #ifndef DEF_Chain
#define DEF_Chain
#include "IncludeDefine.h"
#include "Parameters.h"
#include "ErrorWarning.h"
class OneChain
{
public:
uint bN;
string chr1,chr2;//1/2 (old/new) chr names
vector <uint> bStart1, bStart2, bLen; //blocks starts in 1/2, lengths
};
class Chain {
public:
... |
ed8f2eb4ad4326906e6090dc35c6dd6eca30746fe9cedda4c54221fe756a4a47 | C/C++ | 724 | 38 | // in-memory pooled Reads to reduce new/delete operations
// for each thread, one SISC list is used
#ifndef READ_POOL_H
#define READ_POOL_H
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "read.h"
#include "options.h"
#include "singleproducersingleconsumerlist.h"
using namespace std;
class ReadPoo... |
de150abf6c5f5eb31e61f9593f05056ae3e5c996e208400ea38d6daf730f43e2 | C/C++ | 730 | 34 | /*
* io.h
* peer
*
* Created by Leopold Parts on 13/03/2011.
* Copyright 2011 __MyCompanyName__. All rights reserved.
*
*/
#ifndef PEERUTIL
#define PEERUTIL
#include "vbfa.h"
#include "sparsefa.h"
using namespace PEER;
struct sPeerArgs{
bool no_residuals, no_X, no_W, no_Alpha,no_Z, add_mean, has_header, ... |
ef0056e6579a8bfc42353fe1569300ac8ea822bb0639fcb77f4580d8fd82e392 | C/C++ | 733 | 24 | #ifndef LDA_MODEL_H
#define LDA_MODEL
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include "lda.h"
#include "lda-alpha.h"
#include "cokus.h"
#define myrand() (double) (((unsigned long) randomMT()) / 4294967296.)
#define NUM_INIT 1
void free_lda_model(lda_model*);
void save_lda_model(lda_model*, char*);
... |
358891120360ef2ab845490baf8fde81f971d1f940f8bf84c7d31c265dd1cf6f | C/C++ | 750 | 31 | #pragma once
#ifndef CONVERSION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define CONVERSION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "null.h"
#include "traits.h"
#include <string>
#include <sstream>
namespace YAML
{
inline bool Convert(const std::string& input, std::string& output) {
output = input;
retur... |
ebcb916ff2599567e68c4e79abf8b203b647bf367a9aa3e658944b44ab25e402 | C/C++ | 759 | 38 | #ifndef _MEDAKA_BAMITER_H
#define _MEDAKA_BAMITER_H
#include <stdbool.h>
#include "htslib/sam.h"
// parameters for bam iteration
typedef struct {
htsFile *fp;
sam_hdr_t *hdr;
hts_itr_t *iter;
int min_mapQ;
char tag_name[2];
int tag_value;
bool keep_missing;
const char *read_group;
} mp... |
691b7862379d6cbda9c4ef07be98b9d5ce5e611acb9beee05f9936675a1e0389 | C/C++ | 765 | 36 | #pragma once
#ifndef ITERATOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define ITERATOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
namespace YAML
{
class Node;
struct IterPriv;
class Iterator
{
public:
Iterator();
Iterator(IterPriv *pData);
Iterator(const Iterator& rhs);
~Iterator();
Iterator& operator = ... |
e0538806764488301deda152c7aa45ea47091488032f363577341c383a12d16e | C/C++ | 765 | 37 | #ifndef JSON_REPORTER_H
#define JSON_REPORTER_H
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "options.h"
#include "stats.h"
#include "filterresult.h"
#include <fstream>
#include <atomic>
#include "common.h"
#include "util.h"
using namespace std;
class JsonReporter{
public:
... |
724431c6fd158540752d119f251e0a48c09298332342439309c655ab74582ee8 | C/C++ | 770 | 38 | #pragma once
#ifndef OSTREAM_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define OSTREAM_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include <string>
namespace YAML
{
class ostream
{
public:
ostream();
~ostream();
void reserve(unsigned size);
void put(char ch);
const char *str() const { return m_buffer; }
... |
e25c2390ebd9b48102e51d4cf0f73062cdcd606b7c224e9986610524a0ba4352 | C/C++ | 772 | 29 | #ifndef CODE_ChimericDetection
#define CODE_ChimericDetection
#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ChimericAlign.h"
#include "Genome.h"
class ReadAlign;
class ChimericDetection {
private:
Parameters &P;
ReadAlign *RA;
Transcript ***trAll;
... |
93abbdf14dd518cad566a7c8cc475a37c703c2ec30fe52521af4218a8a1733fa | C/C++ | 777 | 28 | /*
Copyright Rene Rivera 2013-2018
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_DETAIL_ENDIAN_COMPAT_H
#define BOOST_PREDEF_DETAIL_ENDIAN_COMPAT_H
#pragma message("The use of BOOST_*_ENDIAN an... |
8ad963e9ea9eae0912056a1b4cf52743111d676b2707ae5aded5a67876f7b393 | C/C++ | 786 | 31 | #pragma once
#ifndef ITERPRIV_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define ITERPRIV_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "ltnode.h"
#include <vector>
#include <map>
namespace YAML
{
class Node;
// IterPriv
// . The implementation for iterators - essentially a union of sequence and map iterators.
s... |
887278de6eae7ecbbc1cf5193b41088ca7e51b834436ff014652ce57e16cad41 | C/C++ | 788 | 23 | //distance_marcher.h
#pragma once
#include "base_marcher.h"
class distanceMarcher : public baseMarcher
{
public:
distanceMarcher(double *phi, double *dx, long long *flag,
double *distance, int ndim, int *shape,
bool self_test, int order, double narrow,
... |
f876319310d0f3eb405dbd6dbc5c8e7793f360f07497dd46e52e80c7ce5ab77d | C/C++ | 788 | 34 | #ifndef PACKEDARRAY_DEF
#define PACKEDARRAY_DEF
#include "IncludeDefine.h"
class PackedArray {
private:
uint bitRecMask, wordCompLength;
bool arrayAllocated; //true if charArray was allocated
public:
uint wordLength, length, lengthByte;
uint operator [] (uint ii);
char*... |
459946dc8a44334038bd8bbe06eeffb14d1619f6c33a866f6ac059a2182b33ba | C/C++ | 793 | 42 | #ifndef DUPLICATE_H
#define DUPLICATE_H
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "read.h"
#include "options.h"
#include "common.h"
#include <atomic>
using namespace std;
class Duplicate{
public:
Duplicate(Options* opt);
~Duplicate();
bool checkRead(Read* r1);
bool checkPair(... |
76a3c818e46b57ee16ee6614bd8fbc34c96e8885404dc53e24a3305e28cc199c | C/C++ | 793 | 34 | #ifndef MATLAB_BGL_TYPES_H
#define MATLAB_BGL_TYPES_H
/*
* David Gleich
* 19 February 2007
* Copyright, Stanford University, 2007
*/
/**
* @file matlab_bgl_types.h
* Implement a series of types for the matlab_bgl project to support
* large sparse matrices on 64-bit platforms.
*/
/** History
*
* 2007-07-3... |
0c9b461e6b4e28931f3f871bc70bec540a68bc3aaa98181673d7a47cfa2dc95b | C/C++ | 803 | 34 | #ifndef CODE_ClipMate
#define CODE_ClipMate
#include "IncludeDefine.h"
#include "ClipCR4.h"
class ClipMate
{
public:
//clip parameters
int type; //standard sequence clip: 0=5p, 1=3p, -1=no clip; 10/11 = 10X CR4 5/3p clip
uint32 N;
uint32 NafterAd;
string adSeq;
vector<char> adSeqNum;
doubl... |
6958dc50a272b4dd0fd20247769185d53195a3a572cae31c2d1f7723388df758 | C/C++ | 804 | 32 | /*
Copyright Charly Chevalier 2015
Copyright Joel Falcou 2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_HARDWARE_SIMD_ARM_VERSIONS_H
#define BOOST_PREDEF_HARDWARE_SIMD_ARM_VERSIONS_H
#inclu... |
ac05d9bd4b89046b83732e1ccc1706882f7e0a6a2b34b9857e2cbd42b51446ec | C/C++ | 806 | 41 | #ifndef CODE_ClipCR4
#define CODE_ClipCR4
#include "IncludeDefine.h"
#include "opal/opal.h"
class ClipCR4
{
public:
int dbN;//number of sequence in the opal "database"
vector<uint8*> storeClip;
// Results for each sequence in database
vector<OpalSearchResult> opalRes;
OpalSearchResult**... |
15d408dfc448b0fe31cdc8a7863cc3bd2fe7d1fb6811fd8992dd0e17bfc98e51 | C/C++ | 814 | 30 | #pragma once
#include <boost/smart_ptr/intrusive_ptr.hpp>
#include <memory>
#include <string>
namespace asio {
namespace ip {
class tcp;
class udp;
} // namespace ip
class io_context;
} // namespace asio
namespace eos {
class portable_oarchive;
class portable_iarchive;
} // namespace eos
namespace lsl {
/// shared ... |
9518400d8826d8619aaed70b9571cf36858c9c5b923d61a5f8e11462c54a765a | C/C++ | 820 | 38 | #ifndef OVERLAP_ANALYSIS_H
#define OVERLAP_ANALYSIS_H
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <vector>
#include "common.h"
#include "options.h"
#include "read.h"
using namespace std;
class OverlapResult {
public:
bool overlapped;
int offset;
int overlap_len;
... |
c5b8484ce654f546ace537aee3251da9da87a9c37919e21aeee31369efa8e78c | C/C++ | 825 | 23 | /*
Copyright Rene Rivera 2008-2013
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_STD__PREFIX_H
#define BOOST_PREDEF_LIBRARY_STD__PREFIX_H
/*
We need to include an STD header to gives us ... |
01207fbc7682e7a9cc5dfe033d1c894a9bf70070ad842632e18abdf097a42560 | C/C++ | 827 | 27 | #ifndef ADAPTER_TRIMMER_H
#define ADAPTER_TRIMMER_H
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "overlapanalysis.h"
#include "filterresult.h"
#include "options.h"
using namespace std;
class AdapterTrimmer{
public:
AdapterTrimmer();
~AdapterTrimmer();
static bool trimByOverlapAnalys... |
a6dd6d0546be5c6d8956456610a03335972e82154a2eeb2de0da3144f41194fe | C/C++ | 838 | 25 | #ifndef SOCKET_UTILS_H
#define SOCKET_UTILS_H
#include <boost/asio/ip/tcp.hpp>
#include <boost/asio/ip/udp.hpp>
namespace asio = lslboost::asio;
namespace lsl {
inline asio::chrono::milliseconds timeout_sec(double timeout_seconds) {
return asio::chrono::milliseconds(static_cast<unsigned int>(1000 * timeout_seconds)... |
2dad9fd45cbeea617089882ccf3b4cfefaeac6e581cb9ccc58ba63a253efd772 | C/C++ | 840 | 41 | /*
* sim.h
* peer
*
* Created by Leopold Parts on 16/12/2010.
* Copyright 2010 __MyCompanyName__. All rights reserved.
*
*/
#include <Eigen/Eigen>
#include "array_helper.h"
using namespace Eigen;
struct sSimulation {
//resulting expression
PMatrix expr;
//weights
PMatrix W;
//latent factors
PMatrix... |
05ded052748f60b0258196d48a754126919936092ea510b351b1c472954236e5 | C/C++ | 847 | 17 | #ifndef CODE_streamFuns
#define CODE_streamFuns
#include "Parameters.h"
#include <fstream>
unsigned long long fstreamReadBig(std::ifstream &S, char* A, unsigned long long N);
void fstreamWriteBig(std::ofstream &S, char* A, unsigned long long N, std::string fileName, std::string errorID, Parameters &P) ;
fstream &fs... |
586f22b9c3c64da253ce2b518e0fad61f19a7b47b289fc704cc9708242294c49 | C/C++ | 851 | 28 | /* iowin32.h -- IO base function header for compress/uncompress .zip
Version 1.1, February 14h, 2010
part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modification... |
a5059a37836a4a0245c8d61c1da3548a427283a45b190573e24dc816e42248a2 | C/C++ | 857 | 34 | #pragma once
#include <boost/smart_ptr/intrusive_ptr.hpp>
#include <memory>
namespace lslboost {
class thread;
namespace system {
class error_code;
}
namespace asio {
namespace ip {
class tcp;
class udp;
} // namespace ip
class io_context;
} // namespace asio
} // namespace lslboost
namespace eos {
class portable_oa... |
aca85701a0f50bb1bacbc386358e0d3f0ec80f952be8db7b0f020a3b211825ec | C/C++ | 858 | 16 |
#ifdef _MSC_VER
// 4100 - unreferenced formal parameter (occurred e.g. in aligned_allocator::destroy(pointer p))
// 4101 - unreferenced local variable
// 4127 - conditional expression is constant
// 4181 - qualifier applied to reference type ignored
// 4211 - nonstandard extension used : redefined extern to ... |
b1829c6d4169e0d0286ccb83d370b4519685e87d392fcb515352a409bcb29043 | C/C++ | 858 | 25 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#if !defined(BOOST_PREDEF_LIBRARY_STD_H) || defined(BOOST_PREDEF_INTERNAL_GENERATE_TESTS)
#ifndef BOOST_PREDEF_LIBRARY_STD_H
#define BO... |
e4760345b90222ebdb5048c40c33dddb6b443094c0ed4b9078e1c6171b227142 | C/C++ | 863 | 25 | #pragma once
#ifndef EMITTERUTILS_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define EMITTERUTILS_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "ostream.h"
#include <string>
namespace YAML
{
namespace Utils
{
bool WriteString(ostream& out, const std::string& str, bool inFlow, bool escapeNonAscii);
bool WriteSin... |
1140a2a5ae7891b6a8be16ff0f4fe26d89b9d886ff2f3ca31da8b2d40ec256fa | C/C++ | 867 | 31 | #include "cast.h"
#include <iosfwd>
#include <unordered_map>
// Reads an INI file from a stream into a map
class INI {
std::unordered_map<std::string, std::string> values;
template <typename T> inline T convert(const std::string &val) {
return lsl::from_string<T>(val);
}
public:
void load(std::istream &ini);
... |
3c86b6c030dc3a2309cd753fc174810ad250cfe30d3339a372109b91a7c6548c | C/C++ | 880 | 44 | #pragma once
#ifndef SCALAR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define SCALAR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "content.h"
#include <string>
namespace YAML
{
class Scalar: public Content
{
public:
Scalar();
Scalar(const std::string& data);
virtual ~Scalar();
virtual Content *Clone() c... |
7faa0644e58b19e818ad843753dc65f7b40161298a0cf765902cf9ddef66389e | C/C++ | 885 | 46 | #pragma once
#ifndef PARSER_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define PARSER_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "node.h"
#include "noncopyable.h"
#include <ios>
#include <string>
#include <vector>
#include <map>
#include <memory>
namespace YAML
{
class Scanner;
struct ParserState;
struct Token;... |
df698fc4f36b3e04bb2b638c250541027181f9a91066ea35e816f93097a58f04 | C/C++ | 886 | 38 | #include "medaka_bamiter.h"
// a set of strings (with which cffi is happy, avoid exposing kvec_t)
typedef struct {
size_t n_seqs;
char **seqs;
char **names;
_Bool *is_rev;
int *hap;
int *phased_set;
void *t_reads;
} _seq_set;
typedef _seq_set *seq_set;
/** Python wrapper to retrieve_trim... |
4fb9ffd8118f9a97762d392cd5dd950dbdad6cd9888f06119febb4116a98224f | C/C++ | 922 | 36 | #ifndef H_GTF
#define H_GTF
#include "IncludeDefine.h"
#include "Parameters.h"
#include "SjdbClass.h"
#include "Genome.h"
#include "SuperTranscriptome.h"
class GTF {
private:
Genome &genome;
Parameters &P;
string dirOut;
SjdbClass &sjdbLoci;
public:
bool gtfYes;
enum {exT,exS,exE,exG,exL}; /... |
ddd0252a1dd1306d5d8bee794ed20705dea267cce47328f19803449b167c3360 | C/C++ | 923 | 27 | //extension_velocity_marcher.h
#include "distance_marcher.h"
class extensionVelocityMarcher : public distanceMarcher
{
public:
extensionVelocityMarcher(double *phi, double *dx, long long *flag,
double *distance, int ndim, int *shape,
bool self_test,... |
9469bb33e20e44e808ecad51f255edfa2e401ef1e0f01ac28114a52d4f308929 | C/C++ | 928 | 42 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_PYRAMID_H
#define BOOST_PREDEF_ARCHITECTURE_PYRAMID_H
#include <boost/predef/version_number.h>
#inc... |
396c21e01c2b2f9ebbeb184e07f757a625d768fb51b492b4a6199740198324c0 | C/C++ | 932 | 50 | #ifndef LDA_ESTIMATE_H
#define LDA_ESTIMATE_H
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <float.h>
#include <string.h>
#include <time.h>
#include "lda.h"
#include "lda-data.h"
#include "lda-inference.h"
#include "lda-model.h"
#include "lda-alpha.h"
#include "utils.h"
#include "cokus.h"
int LAG... |
d3e6302d6809b8858e78ec5a8ac7fd0d18e0c087f55c275d79ceb74061f2528f | C/C++ | 933 | 27 | #ifndef H_SoloReadBarcodeStats
#define H_SoloReadBarcodeStats
#include "IncludeDefine.h"
class SoloReadBarcodeStats {
public:
vector<string> names;
enum { noNoAdapter, noNoUMI, noNoCB, noNinCB, noNinUMI, noUMIhomopolymer, noNoWLmatch, noTooManyMM, noTooManyWLmatches, yesWLmatchExact, ye... |
228b80f17ee30f2d9c363272dd88ed6d6782da45f068ce27f5ba2be00e05e83a | C/C++ | 935 | 38 | /*
Copyright Charly Chevalier 2015
Copyright Joel Falcou 2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_HARDWARE_SIMD_ARM_VERSIONS_H
#define BOOST_PREDEF_HARDWARE_SIMD_ARM_VERSIONS_H
#inclu... |
6e06f02b6ee36be68a0e1d68e31e1e437bd6398785f5eac26e7f49c5b079fcd3 | C/C++ | 935 | 42 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_Z_H
#define BOOST_PREDEF_ARCHITECTURE_Z_H
#include <boost/predef/version_number.h>
#include <boost/... |
8fb4528b7252d88acf177cddc3e13e500bce647705f019b1585afe76883cf1de | C/C++ | 935 | 42 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LANGUAGE_OBJC_H
#define BOOST_PREDEF_LANGUAGE_OBJC_H
#include <boost/predef/version_number.h>
#include <boost/pr... |
f35e70b6359a919b9adccf3cb6f625a0ba6c8344098526fd637f4c84b58af710 | C/C++ | 936 | 18 | #ifndef CODE_SuffixArrayFuns
#define CODE_SuffixArrayFuns
#include "IncludeDefine.h"
#include "Parameters.h"
#include "PackedArray.h"
#include "Genome.h"
uint medianUint2(uint, uint);
uint compareSeqToGenome(Genome &mapGen, char** s2, uint S, uint N, uint L, uint iSA, bool dirR, bool& comparRes);
uint findMultRange(G... |
21d920f21ad199d9068a4da5507e4a0f835d313d04907593fe3540ecbbe3e734 | C/C++ | 937 | 27 | #ifndef COKUS_H
#define COKUS_H
#include <stdio.h>
#include <stdlib.h>
//
// uint32 must be an unsigned integer type capable of holding at least 32
// bits; exactly 32 should be fastest, but 64 is better on an Alpha with
// GCC at -O3 optimization so try your options and see what's best for you
//
typedef unsigned l... |
cd09b75ad62d3e892ecb314f746ec4c19b0706e9fd615f7d69bfc77f097a540b | C/C++ | 948 | 41 | #ifndef CODE_ParametersChimeric
#define CODE_ParametersChimeric
#include "IncludeDefine.h"
class Parameters;
class ParametersChimeric
{//
public:
uint segmentMin, junctionOverhangMin; //min chimeric donor/acceptor length
uint segmentReadGapMax; //max read gap for stitching chimeric windows
... |
10ae700fcf9333edb28c08b16daad44e8dac98cc9f8ff886f294563aa0b063cf | C/C++ | 953 | 32 | /*
Copyright Rene Rivera 2008-2015
Copyright Franz Detro 2014
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#if !defined(BOOST_PREDEF_OS_H) || defined(BOOST_PREDEF_INTERNAL_GENERATE_TESTS)
#ifndef BOOST_PREDEF_OS_H
... |
6dc15acfc25a70692cdfe3cce52c629026d5e316f59bfa379bb5889e7c097900 | C/C++ | 957 | 53 | /*
* Copyright 1996-2006 Catherine Loader.
*/
/*
* Copyright (c) 1998-2006 Catherine Loader
* See README file for details.
*
*
* Headers for the tube library.
*/
#ifndef I_TUBE_H
#define I_TUBE_H
/*
* public functions needed by routines calling the tube library.
*/
extern double critval();
extern doub... |
1f5c1f7743dcea271dd1ba7847bece768049cacea00d22bdfb4a71ef7f7a9c7a | C/C++ | 958 | 24 | #ifndef SOCKET_UTILS_H
#define SOCKET_UTILS_H
#include <asio/ip/tcp.hpp>
#include <asio/ip/udp.hpp>
using udp_socket = asio::basic_datagram_socket<asio::ip::udp, asio::io_context::executor_type>;
using tcp_socket = asio::basic_stream_socket<asio::ip::tcp, asio::io_context::executor_type>;
using tcp_acceptor = asio::b... |
775a9b4ed469a4d2baffb38525a8b086f58cb95ff39e00f6f4dab46e443705a6 | C/C++ | 958 | 41 | /*
Copyright Zhang Na 2022
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_LOONGARCH_H
#define BOOST_PREDEF_ARCHITECTURE_LOONGARCH_H
#include <boost/predef/version_number.h>
#include... |
36ee0b28d38b4655771a0ff113a770281994f79f35f131d29e9fe0db3a001854 | C/C++ | 960 | 38 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#include <boost/predef/architecture/x86/32.h>
#include <boost/predef/architecture/x86/64.h>
#ifndef BOOST_PREDEF_ARCHITECTURE_X86_H
#... |
e3cc8a7aee08b0ebb44c05ae9499b4780abdf7304090a3a4c59f130be6878777 | C/C++ | 960 | 43 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LANGUAGE_OBJC_H
#define BOOST_PREDEF_LANGUAGE_OBJC_H
#include <boost/predef/version_number.h>
#include <boost/pr... |
bc4e340ccc90eb02b090db5d53d9bbd8f9142badcb7d326fa11d504e680a09d3 | C/C++ | 966 | 24 | /*
bgmg - tool to calculate log likelihood of BGMG and UGMG mixture models
Copyright (C) 2018 Oleksandr Frei
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License... |
a8e355739f83429d440605137f18a163b53d88b7d6f0ea54d77f85ea6d12193e | C/C++ | 967 | 31 | // Copyright Antony Polukhin, 2016-2022.
//
// Distributed under the Boost Software License, Version 1.0. (See
// accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
// No include guards! Intentionally.
// Link or header only
#if !defined(BOOST_STACKTRACE_LINK) && defined(BOOST_STACK... |
8ee091edb9058eb7f44a5c0b9a174bddd2434754b9fa9781b28ebabe240cf082 | C/C++ | 985 | 38 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#include <boost/predef/architecture/x86/32.h>
#include <boost/predef/architecture/x86/64.h>
#ifndef BOOST_PREDEF_ARCHITECTURE_X86_H
#... |
1bbaf57dde57a7acd662a15d5e344e5ed6c43d6d08896618c3730ceb0a131394 | C/C++ | 987 | 44 | /*
Copyright Benjamin Worpitz 2018
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_PTX_H
#define BOOST_PREDEF_ARCHITECTURE_PTX_H
#include <boost/predef/version_number.h>
#include <bo... |
16b24b55d562c961666371f669d2a6c07d09bedea5e6a33d0647536179ef04f9 | C/C++ | 988 | 30 | //===----------------------------------------------------------------------===//
//
// The LLVM Compiler Infrastructure
//
// This file is dual licensed under the MIT and the University of Illinois Open
// Source Licenses. See LICENSE.TXT for details.
//
//===----------------------------------------... |
fdde4c571c2ec8107ab5e4c16b215e4260e5905e7fa3e5958500f9c638d4dfeb | C/C++ | 988 | 37 | #pragma once
#ifndef PARSERSTATE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define PARSERSTATE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include <string>
#include <map>
#include <stack>
#include <cassert>
namespace YAML
{
struct Version {
bool isDefault;
int major, minor;
};
struct ParserState
{
enum COLLECT... |
e42157ef2328bf9247d6bf3eb8198b7f9224c70246c27fa983cb5d66f8f03e4c | C/C++ | 990 | 33 | /*
Copyright Rene Rivera 2008-2015
Copyright Franz Detro 2014
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#if !defined(BOOST_PREDEF_OS_H) || defined(BOOST_PREDEF_INTERNAL_GENERATE_TESTS)
#ifndef BOOST_PREDEF_OS_H
... |
bc7e7d0a6cb2411b653c98b6e3694d3e31e95723c0fe0ea09d41eddb91a92c6a | C/C++ | 996 | 33 | #ifndef H_SoloFilteredCells
#define H_SoloFilteredCells
class SoloFilteredCells {
public:
array<uint64,13> C;
uint64 &nCells =C[0];
uint64 &nReadInCells =C[1];
uint64 &medianReadPerCellUnique =C[2];
uint64 &meanReadPerCellUnique =C[3];
uint64 &nUMIinCells ... |
70ddfa8e8900bb4ce7665f5390602198a139a86ef04590eaa9b6b5a9620eff27 | C/C++ | 1,001 | 45 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_BEOS_H
#define BOOST_PREDEF_OS_BEOS_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.h>... |
74696b064252382e97e8fe0a6892f24e1d41f71fb31606665967be14259a3577 | C/C++ | 1,005 | 28 | /*
Copyright Rene Rivera 2013-2015
Copyright (c) Microsoft Corporation 2014
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#if !defined(BOOST_PREDEF_PLATFORM_H) || defined(BOOST_PREDEF_INTERNAL_GENERATE_TESTS)
#ifnde... |
d050591a26103738a1aa9281c1399decef7c9eaed477cb390f1fdaf8bfffc3fc | C/C++ | 1,008 | 28 | /*
Copyright Rene Rivera 2013-2015
Copyright (c) Microsoft Corporation 2014
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#if !defined(BOOST_PREDEF_PLATFORM_H) || defined(BOOST_PREDEF_INTERNAL_GENERATE_TESTS)
#ifnde... |
5d08fc91d7ca55900469853bf4a15d120081e161c9f7600b5659e526cee7474a | C/C++ | 1,023 | 44 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_STD_VACPP_H
#define BOOST_PREDEF_LIBRARY_STD_VACPP_H
#include <boost/predef/library/std/_prefix.h>
#inc... |
25bed579ff9afd602182af9f322fffcdfc4994f62ed1a1cc20379c24a706794b | C/C++ | 1,026 | 46 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_BEOS_H
#define BOOST_PREDEF_OS_BEOS_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.h>... |
cc31820d250a50ea22d70f89653c103e02e5ab80fb0bbefed3a6f711f3893326 | C/C++ | 1,027 | 45 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_OS400_H
#define BOOST_PREDEF_OS_OS400_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.... |
cfb8ec651c239b38bb1c15b9d917b4d0e9e028a5ee0ddebe6e3ddc8f8dd0e166 | C/C++ | 1,031 | 43 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_SYS390_H
#define BOOST_PREDEF_ARCHITECTURE_SYS390_H
#include <boost/predef/version_number.h>
#inclu... |
0d2ae912d5288c0b03983e4562fb60725eec8022be47387b01bfc04e356779b9 | C/C++ | 1,033 | 43 | /*
Copyright 2017 James E. King, III
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_PLAT_CLOUDABI_H
#define BOOST_PREDEF_PLAT_CLOUDABI_H
#include <boost/predef/version_number.h>
#inclu... |
1ed1cbaef9c42a086e3e174decb10dfd90dfc30b2fc404e5249540072103530c | C/C++ | 1,033 | 43 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_SYS370_H
#define BOOST_PREDEF_ARCHITECTURE_SYS370_H
#include <boost/predef/version_number.h>
#inclu... |
05c0c8b07c74c4f036fc5a0f5e212a754fc313b9d6d07ce560e0662f1f0d8792 | C/C++ | 1,034 | 47 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_C_VMS_H
#define BOOST_PREDEF_LIBRARY_C_VMS_H
#include <boost/predef/library/c/_prefix.h>
#include <boos... |
97234e497860c29edf0ca0851737e62329895fbda7e0810d722f0c890b4847f7 | C/C++ | 1,035 | 26 | namespace internal {
// TODO : move this to GivensQR once there's such a thing in Eigen
template <typename Scalar>
void r1mpyq(DenseIndex m, DenseIndex n, Scalar *a, const std::vector<JacobiRotation<Scalar> > &v_givens, const std::vector<JacobiRotation<Scalar> > &w_givens)
{
typedef DenseIndex Index;
/* ... |
c67dd213a8e36ab432e46a4e8358398f505d67c6dd4a3e0c3d2d131a29e63c8b | C/C++ | 1,038 | 33 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu)
// This file is part of MMLDA-C.
// MMLDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (at your
// option) any... |
ce290b122359c630d608ce552f17e14a0eba0b69a095e121b09dee0ea7924eff | C/C++ | 1,042 | 45 | #pragma once
#ifndef STRINGSOURCE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define STRINGSOURCE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include <cstddef>
namespace YAML
{
class StringCharSource
{
public:
StringCharSource(const char *str, std::size_t size): m_str(str), m_size(size), m_offset(0) {}
operator boo... |
fae11680f886c8cc09cfbb35a84e542283233cfc87dc9276a11ea885765b9692 | C/C++ | 1,043 | 49 | #pragma once
namespace plog
{
enum Severity
{
none = 0,
fatal = 1,
error = 2,
warning = 3,
info = 4,
debug = 5,
verbose = 6
};
inline const char* severityToString(Severity severity)
{
switch (severity)
... |
810361cf184818e2da9525cc6e22b5523e5efea70d73420c438829f4ea3ac331 | C/C++ | 1,048 | 46 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_IRIX_H
#define BOOST_PREDEF_OS_IRIX_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.h>... |
13d96dc28a0acb8fa6781acd0ddaaa4b41b38059fe5aff8303412380520c48b4 | C/C++ | 1,050 | 45 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_STD_VACPP_H
#define BOOST_PREDEF_LIBRARY_STD_VACPP_H
#include <boost/predef/library/std/_prefix.h>
#inc... |
39b086e860bbef79d3fa99182940d6b7f6c2a555d521923cd7bc2103770e2ccc | C/C++ | 1,050 | 46 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_STD_CXX_H
#define BOOST_PREDEF_LIBRARY_STD_CXX_H
#include <boost/predef/library/std/_prefix.h>
#include... |
8b383d8212721639ffd5d9205800e4a5734269b3821a3502316e986dd64582bc | C/C++ | 1,052 | 46 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_OS400_H
#define BOOST_PREDEF_OS_OS400_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.... |
8361c3f4e318fbfcdf4e7794d34e3dec006f03926d6fc48e44c584084b9fa128 | C/C++ | 1,056 | 44 | /*
Copyright Rene Rivera 2015-2019
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_PLAT_ANDROID_H
#define BOOST_PREDEF_PLAT_ANDROID_H
#include <boost/predef/version_number.h>
#include <boost/pred... |
14a99fdd8aabc22a0cc7c28263b5776fcfe6f56491ad429f0dfd8e0548cb091e | C/C++ | 1,057 | 48 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_C_VMS_H
#define BOOST_PREDEF_LIBRARY_C_VMS_H
#include <boost/predef/library/c/_prefix.h>
#include <boos... |
7234417663ea17357e7d2f48081e87865fb52af0773632c9c50ff08088ab884b | C/C++ | 1,058 | 44 | /*
Copyright 2017 James E. King, III
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_PLAT_CLOUDABI_H
#define BOOST_PREDEF_PLAT_CLOUDABI_H
#include <boost/predef/version_number.h>
#inclu... |
acce0b8715c11924176a0438cbcbc144fb13c2f583cb6131f518538561e0c042 | C/C++ | 1,060 | 32 | /*
* The design structure used in Locfit, and associated macro definitions.
*/
typedef struct {
int des_init_id;
double *wk;
Sint *ind;
int lwk, lind;
double *xev; /* fitting point, length p */
double *X; /* design matrix, length n*p */
double *w, *di,... |
593ec94fae8419700ac96a7ad3831aada0691bbbaa135cef1b57dc222aeddc20 | C/C++ | 1,063 | 45 | /**
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#pragma once
#include <cstdint>
#include <istream>
#include <ostream>
#include <vector>
#include <assert.h>
#i... |
f5f56d447f8d3ce785debeabaa914678d20d9a0a736471d9698d62a44ca359bb | C/C++ | 1,065 | 47 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_IRIX_H
#define BOOST_PREDEF_OS_IRIX_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.h>... |
75313ece35b37cee46ca628fa2a81e435d545b59510beeedc5c18c8edc27f338 | C/C++ | 1,067 | 45 | /*
Copyright Rene Rivera 2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_ANDROID_H
#define BOOST_PREDEF_OS_ANDROID_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.h... |
12a110643f309d622b5e8d3f5acbf8d74ef45baed0c63a7c8d3c99b3e4c541fc | C/C++ | 1,068 | 46 | /*
Copyright Jessica Hamilton 2014
Copyright Rene Rivera 2014-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_HAIKU_H
#define BOOST_PREDEF_OS_HAIKU_H
#include <boost/predef/version_number... |
c0b29d567f566ab8e6e2d4322762a2adb814eb40291a4579b9f55e760f2bdcc7 | C/C++ | 1,070 | 46 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_LINUX_H
#define BOOST_PREDEF_OS_LINUX_H
#include <boost/predef/version_number.h>
#include <boost/predef/make.... |
6ec5c85e6860922a1f85b5fb28752e9ebb79581294651f4dfbb0be6337d01a98 | C/C++ | 1,071 | 33 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu), Xiuming Zhang
// This file is part of POLARLDA-C.
// POLARLDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (a... |
f3ab03377804b86686638b12e4f189917063552f218cc2b82b3e0e961c52a396 | C/C++ | 1,071 | 38 | #ifndef EVALUATOR_H
#define EVALUATOR_H
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "options.h"
#include "util.h"
#include "read.h"
using namespace std;
class Evaluator{
public:
Evaluator(Options* opt);
~Evaluator();
// evaluate how many reads are stored in the input file
void e... |
0cf53f7a39b3131dc3e48f11c4a7fb7628f33b78783f399d919ae590d11bda3c | C/C++ | 1,074 | 47 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_STD_CXX_H
#define BOOST_PREDEF_LIBRARY_STD_CXX_H
#include <boost/predef/library/std/_prefix.h>
#include... |
df90063aab9c2e0d714a85089ac8909f33cb40be33e7c76615abce51fa659cb5 | C/C++ | 1,083 | 66 | #ifndef FASTA_READER_H
#define FASTA_READER_H
// includes
#include <cctype>
#include <clocale>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <stdexcept>
#include <string>
#include <map>
using namespace std;
class FastaReader
{
public:
FastaReader(string fastaFile, bool forceUpperCase = true)... |
ffa42475fc756412f405e8ae0033620968fb8e451e3482d6f25afa8c8b5af0e7 | C/C++ | 1,084 | 48 | /*
Copyright Rene Rivera 2011-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_PYRAMID_H
#define BOOST_PREDEF_ARCHITECTURE_PYRAMID_H
#include <boost/predef/version_number.h>
#inc... |
f990aec262fa78ee04746b90aafff3cfd8408fe90e5c1af71cd5ae67bbafadea | C/C++ | 1,085 | 48 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_Z_H
#define BOOST_PREDEF_ARCHITECTURE_Z_H
#include <boost/predef/version_number.h>
#include <boost/... |
c8384457cd8fa97ee99d705075b930ebfb6666872161b68fab0581f1cfc3d63a | C/C++ | 1,093 | 47 | /*
Copyright Jessica Hamilton 2014
Copyright Rene Rivera 2014-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_OS_HAIKU_H
#define BOOST_PREDEF_OS_HAIKU_H
#include <boost/predef/version_number... |
d99105bb5c13cfbeba54ec679395ed36306a734e2ecce21383a74d7eaf03fa78 | C/C++ | 1,093 | 48 | /*
Copyright Andreas Schwab 2019
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_ARCHITECTURE_RISCV_H
#define BOOST_PREDEF_ARCHITECTURE_RISCV_H
#include <boost/predef/version_number.h>
#include <... |
06c82b6697ed9bf3814cc2708147474f783be22853bfd074853a59d462b97bfa | C/C++ | 1,102 | 47 | /*
Copyright Rene Rivera 2008-2015
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
*/
#ifndef BOOST_PREDEF_LIBRARY_C_UC_H
#define BOOST_PREDEF_LIBRARY_C_UC_H
#include <boost/predef/library/c/_prefix.h>
#include <boost/... |
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