sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0fab1ee4fb2fdb0fd2f8323a6dfc1e88785a6669fbf484a85b14429f4f4639e9 | C++ | 14,919 | 313 | #include "MetalLSTMCaller.h"
#include "MetalCallerTask.h"
#include "basecall/crf_utils.h"
#include "decode/beam_search.h"
#include "model/MetalCRFModel.h"
#include "torch_utils/metal_utils.h"
#include "utils/math_utils.h"
#include "utils/memory_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <casse... |
459d030550f6561200f010ebd10adfa113a8902ff40219d35dd6dd2b85c228e7 | C++ | 15,000 | 375 | #include "read_output_progress_stats.h"
#include "utils/thread_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cassert>
#include <cmath>
#include <limits>
#include <sstream>
namespace dorado {
namespace {
const std::string PREFIX_PROGRESS_LINE_HDR{"[PROG_STAT_HDR] "};
const std::string PREFIX_P... |
6cb7789ea2f3b8a6afc5e42597872f19ef46f2def5f494141e70acc42a0e0823 | C++ | 15,155 | 389 | #include "encoder_counts.h"
#include "medaka_counts.h"
#include <spdlog/spdlog.h>
#include <torch/types.h>
#include <cassert>
#include <cstddef>
#include <stdexcept>
namespace dorado::secondary {
namespace {
/**
* \brief Converts the vectors produced by the pileup function into proper tensors.
*/
CountsResult c... |
973a26564ddc2613acdb3fa5d4d4264873b3d2e4bb256243620dd5d97a717e49 | C++ | 15,270 | 450 | #include "utils/SampleSheet.h"
#include "utils/PostCondition.h"
#include "utils/string_utils.h"
#include "utils/types.h"
#include <algorithm>
#include <fstream>
#include <iostream>
#include <iterator>
#include <set>
#if defined(__GNUC__) && !defined(__clang__) && !defined(__INTEL_COMPILER)
#pragma GCC diagnostic pus... |
e7a523f7cb2aedc31bae3b53209073ea2b6540cea6ad0401df387316916a45a5 | C++ | 15,508 | 519 | /****************************************************************************
**
** Copyright (c) 2008-2018 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullFacet.cpp#6 $$Change: 2549 $
** $DateTime: 2018/12/28 22:24:20 $$Author: bbarber $
**
*********************************************... |
e3bbd332a3baa823a49716582eb84506fe6c8c3c7d55945ed39287574927d35b | C++ | 16,029 | 334 | #include "bam_tagging.h"
#include "cli.h"
#include "faidx_utils.h"
#include "haplotag_lib/string_utils.h"
#include "kadayashi_utils.h"
#include "local_haplotagging.h"
#include "pipeline.h"
#include "resources.h"
#include "secondary/common/bam_file.h"
#include <htslib/faidx.h>
#include <htslib/sam.h>
#include <spdlog/s... |
8fd7338f6debdf456570f8bf8117731d0766282af0e685e95710594e47f75af1 | C++ | 16,060 | 361 | #include "poly_tail/poly_tail_calculator.h"
#include "dna_poly_tail_calculator.h"
#include "plasmid_poly_tail_calculator.h"
#include "poly_tail/poly_tail_config.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "rna_poly_tail_calculator.h"
#include "utils/log_utils.h"
#include "utils/math_utils.h"
#incl... |
25cd5139b1ebd0f28536c57228b349e4fb88243632bbf28c388d26ecc5b8e956 | C++ | 16,537 | 408 | #include "torch_utils/trim.h"
#include "TestUtils.h"
#include "demux/Trimmer.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "read_pipeline/base/read_utils.h"
#include "utils/types.h"
#include <ATen/TensorIndexing.h>
#include <catch2/catch_test_macros.hpp>
#i... |
2aafffb7ad668377923394772a03181adc96f343eb797d696d092c158dd14b78 | C++ | 16,889 | 371 | #include "demux/AdapterDetector.h"
#include "adapter_primer_kits.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include "utils/string_utils.h"
#include "utils/types.h"
#include <edlib.h>
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <string>
#include <string_vie... |
b44c3d01a5ff4ba9f7d0aab9d79a7a13edeaf5afd8b7557c449c7381c87f6aba | C++ | 17,001 | 424 | #include "config/BasecallModelConfig.h"
#include "TestUtils.h"
#include "models/kits.h"
#include "utils/parameters.h"
#include <catch2/catch_test_macros.hpp>
#include <torch/torch.h>
#include <filesystem>
#include <stdexcept>
#include <string>
#define CUT_TAG "[BasecallModelConfig]"
using namespace dorado::config;... |
96103948d6b32bf8cbded2da88d5a209e837c15ff9b7f37c28c62ad9d51f153d | C++ | 17,055 | 412 | #include "secondary/consensus/variant_calling_sample.h"
#include "secondary/consensus/consensus_utils.h"
#include "secondary/consensus/sample.h"
#include "secondary/consensus/sample_trimming.h"
#include "secondary/features/decoder_base.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <sstream>
#include <s... |
77dda6754a7ea3c9e20d2c28cf4462e3e07fce26d5e3e735d39a4c0b68b59134 | C++ | 17,170 | 410 | #include "ProgressTracker.h"
#include "basecall_output_args.h"
#include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "demux/KitInfoProvider.h"
#include "demux/barcoding_info.h"
#include "demux/parse_custom_kit.h"
#include "dorado_version.h"
#include "hts_utils/HeaderMapper.h"
#include "hts_utils/KString.h"
#in... |
542a97c6c88e4531a08346d9e8da63e0c0599af14a7232f878fab398d1f9833f | C++ | 17,500 | 410 | #include "ProgressTracker.h"
#include "alignment/alignment_info.h"
#include "alignment/minimap2_args.h"
#include "basecall_output_args.h"
#include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "dorado_version.h"
#include "hts_utils/HeaderMapper.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/hts_types.h... |
aa419239c0e74967cf32b1996825928f640b2ae3485636bb5d35fbf41a15aec0 | C++ | 17,787 | 437 | #include "model_resolver/ModelResolver.h"
#include "config/BasecallModelConfig.h"
#include "file_info/file_info.h"
#include "model_downloader/model_downloader.h"
#include "models/kits.h"
#include "models/metadata.h"
#include "models/model_complex.h"
#include "models/models.h"
#include "utils/math_utils.h"
#include "ut... |
ca3a496efdc34444a161e11ba11f750587d3fee940e23d00f483c53cf53884b5 | C++ | 17,881 | 480 | #include "models/kits.h"
#include "utils/string_utils.h"
#include <algorithm>
#include <array>
#include <cstdlib>
#include <stdexcept>
#include <string>
namespace dorado::models {
using FC = Flowcell;
using KC = KitCode;
template <typename Code, typename Info>
Code get_code(const std::string& str,
Co... |
093d08513925f23363052f212a4c54e69203c2aeb28382fd5f4460fe3eeb9472 | C++ | 18,136 | 456 | #include "torch_utils/metal_utils.h"
// A header included by IOKitLib.h uses #if instead of #ifdef for an
// undefined macro - which we warn about - so ignore that warning.
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wundef"
#include <IOKit/IOKitLib.h>
#pragma clang diagnostic pop
#include "utils... |
e074cdeb6c632cc0873699028cee7ac292b9749b5e33d930affd4137e10b00ad | C++ | 18,316 | 556 | #include "TestUtils.h"
#include "secondary/architectures/model_config.h"
#include "secondary/architectures/model_config_validation.h"
#include <catch2/catch_test_macros.hpp>
#include <toml.hpp>
#include <filesystem>
#include <fstream>
#include <string>
#include <unordered_map>
#include <utility>
#include <vector>
na... |
e12e272875e629ed747d94262dbdf93eaecb42d1a3c8afba589ce5e37a5bfb23 | C++ | 18,319 | 444 | #include "hts_writer/SummaryFileWriter.h"
#include "hts_utils/bam_utils.h"
#include "hts_writer_utils.h"
#include "utils/barcode_kits.h"
#include "utils/string_utils.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <array>
#include <fstream>
#include <iomanip>
#include <ostream>
#include <string_view>
... |
7d53982ee2d49dca7ae2d354588c176e423869434bb6b717e5aad03c13691faf | C++ | 18,987 | 428 | #include "secondary/common/variant.h"
#include "secondary/consensus/variant_calling.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <spdlog/spdlog.h>
#include <cstdint>
#include <numeric>
#include <string>
#include <vector>
namespace dorado::secondary::consensus:... |
913f0bc08a0fc368c6ebfad9c4ef551bdc33a7734ab27c6057c54edac8ebf94f | C++ | 19,340 | 521 | #include "secondary/consensus/sample_trimming.h"
#include <spdlog/spdlog.h>
#include <ostream>
#include <sstream>
#include <stdexcept>
#include <string>
#include <tuple>
namespace dorado::secondary {
namespace {
enum class Relationship {
DIFFERENT_REF_NAME,
FORWARD_OVERLAP,
REVERSE_OVERLAP,
FORWARD... |
da5e3b1512ad7aaf6ded5430eda7cc1d209995bb259c5b71c317c04298773434 | C++ | 19,641 | 451 | #include "hts_utils/bam_utils.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/types.h"
#include <ATen/ops/empty.h>
#include <catch2/catch_message.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
#inc... |
b1c63e85e5485163db952bb8b6da8bc73e00226620f19b315a9e91137b8d0de6 | C++ | 20,054 | 504 | #include "correct/features.h"
#include "correct/conversions.h"
#include "correct/types.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h"
#include "torch_utils/gpu_profiling.h"
#include "utils/cigar.h"
#include "utils/sequence_utils.h"
#include <ATen/Tensor.h>
#include <ATen/ops/empty.h>
#include <ATen/... |
749084d4a10b36184ff65bbf9a741018fcad62d2167189b851f916aeb82a69bc | C++ | 20,244 | 480 | #include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "api/runner_creation.h"
#include "config/BasecallModelConfig.h"
#include "config/ModBaseBatchParams.h"
#include "demux/adapter_info.h"
#include "demux/barcoding_info.h"
#include "demux/parse_custom_kit.h"
#include "demux/parse_custom_sequences.h"
#include "m... |
d421325f78981c6710c67d50f9a6bc417701009f49bfd49373ac0fbab66b40f2 | C++ | 20,390 | 508 | #include "utils/sequence_utils.h"
#include "utils/log_utils.h"
#include "utils/simd.h"
#include <edlib.h>
#include <minimap.h>
#include <nvtx3/nvtx3.hpp>
#include <algorithm>
#include <array>
#include <cassert>
#include <cmath>
#include <cstdint>
#include <cstring>
#include <iterator>
#include <numeric>
#include <op... |
47541df13c4b3c1ee1162b4b1a9a2240160dad43967c1e3cff8c371337d239c6 | C++ | 21,327 | 495 | #include "secondary/architectures/model_config_validation.h"
#include <toml.hpp>
#include <iterator>
#include <stdexcept>
#include <string>
#include <unordered_map>
#include <utility>
#include <vector>
namespace dorado::secondary {
namespace {
using ParamSpecs = std::vector<VersionedParamSpec>;
using SpecMap = std:... |
d71cbdb1100010991753e4b3b80b8866265d97a08855f0b8ff1e41c00c91f6b2 | C++ | 21,651 | 462 | #include "nn/ConvStack.h"
#include "config/common.h"
#include "nn/KoiUtils.h"
#include "torch_utils/gpu_profiling.h"
#if DORADO_CUDA_BUILD
extern "C" {
#include "koi.h"
}
#endif
#include <torch/nn.h>
namespace dorado::nn {
#if DORADO_CUDA_BUILD
namespace {
KoiActivation get_koi_activation(config::Activation act)... |
5db12169f5eb376bfa70425a5f17fa31eab6be5d027d681caec81dd105ba35e0 | C++ | 21,796 | 526 | #include "read_pipeline/base/messages.h"
#include "hts_utils/bam_utils.h"
#include "modbase/ModBaseContext.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/ReadPair.h"
#include "read_pipeline/base/messages/Simplex... |
0addf4206de1f6590fe3f9444e6d94288b107341d8ee1e9cf6f08ebb61d62c07 | C++ | 21,873 | 536 | #include "encoder_read_alignment.h"
#include "local_haplotagging.h"
#include "secondary/features/encoder_utils.h"
#include "secondary/features/kadayashi_utils.h"
#include "secondary/features/medaka_read_matrix.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include "utils/container_uti... |
f3730c0daeb5e71621fe392ef1103322cb788060d6a7df1e9549d90fed40a4a1 | C++ | 21,949 | 487 | #include "TestUtils.h"
#include "model_resolver/ModelResolver.h"
#include "models/kits.h"
#include "models/metadata.h"
#include "models/model_complex.h"
#include "models/models.h"
#include "utils/fs_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <iterator>
... |
79141f6b2954e58379e8120c2e55a243bd8d11fdfaf2b60853ea1b32e595ea86 | C++ | 22,206 | 584 | #include "read_pipeline/nodes/CorrectionInferenceNode.h"
#include "correct/decode.h"
#include "correct/features.h"
#include "correct/infer.h"
#include "correct/windows.h"
#include "hts_utils/FastxRandomReader.h"
#include "hts_utils/hts_types.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h"
#include "se... |
eb3f5e449ced47e59dcd3628e19b1707f27a977ca206ef373001b22958f0034e | C++ | 22,284 | 584 | #include "config/ModBaseModelConfig.h"
#include "config/common.h"
#include "hts_utils/bam_utils.h"
#include "utils/dev_utils.h"
#include "utils/sequence_utils.h"
#include <spdlog/spdlog.h>
#include <toml.hpp>
#include <numeric>
#include <optional>
#include <stdexcept>
#include <string>
#include <vector>
namespace ke... |
05601fbe791b71e277ecd17c7370a76630e7441b46abffddd0d5f3c8a2bfcd66 | C++ | 22,487 | 611 | #include "hts_utils/bam_utils.h"
#include "hts_utils/KString.h"
#include "utils/sequence_utils.h"
#include "utils/string_utils.h"
#include <edlib.h>
#include <htslib/sam.h>
#include <algorithm>
#include <bitset>
#include <cassert>
#include <cctype>
#include <cmath>
#include <cstdint>
#include <iostream>
#include <ma... |
074b9d7c6a0843e97501648ac211869e950cefa5e4c3bda6db6bd8e0ba39626d | C++ | 22,641 | 576 | #include "CorrectionMapper.h"
#include "CorrectionPafReader.h"
#include "CorrectionProgressTracker.h"
#include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "dorado_version.h"
#include "hts_utils/fai_utils.h"
#include "model_downloader/model_downloader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "r... |
03a2e7e9541b23ed0a8520787062d0d69812f91c77cac1dd647c1af6d70bea0e | C++ | 22,836 | 530 | #include "hts_utils/HeaderMapper.h"
#include "TestUtils.h"
#include "hts_utils/KString.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/hts_types.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages.h"
#include "read_pipeline/base/termin... |
493186872cc3ffb0716f2c45b8466c8d9231b2a3e59adb7122621b6c48666c98 | C++ | 24,254 | 652 | #include "hts_utils/hts_file.h"
#include "hts_utils/bam_utils.h"
#include "utils/PostCondition.h"
#include <htslib/bgzf.h>
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <array>
#include <cassert>
#include <filesystem>
#include <map>
#include <stdexcept>
namespace {
constexpr s... |
149143cbaebd717db7db02f8cdeb3456d3f222236f9dc21e3481e72ded4899d4 | C++ | 24,562 | 553 | #include "demux/BarcodeClassifier.h"
#include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "demux/barcoding_info.h"
#include "demux/parse_custom_kit.h"
#include "demux/parse_custom_sequences.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/HtsRe... |
03e85858735193afb862284b97fc1cb0215c4e1b5dd37885723e762659a4c538 | C++ | 24,565 | 675 | #include "aligner/Minimap2Aligner.h"
#include "alignment/sam_utils.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/messages.h"
#include "read_pipeline/base/messages/ReadCommon.h"
#include "utils/PostCondition.h"
#include "utils/sequence_utils.h"
#include <htslib/sam.h>
#include <minimap.h>
#include ... |
4c140f0362d138b2e0d71f14b62f93bae54b25ac86126eacd5cfe66b432a0176 | C++ | 24,776 | 549 | #include "read_pipeline/nodes/PairingNode.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages/ReadPair.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include "utils/thread_utils.h"
#include <minimap.h>
#include <n... |
252d8af50733b7d8c3ae2137bacea296067316190668cc732d07d61bdf8adb26 | C++ | 25,764 | 607 | #include "hts_utils/HeaderMapper.h"
#include "hts_utils/FastxSequentialReader.h"
#include "hts_utils/MergeHeaders.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/fastq_tags.h"
#include "hts_utils/header_utils.h"
#include "hts_utils/hts_types.h"
#include "hts_utils/sequence_file_format.h"
#include "utils/Sample... |
bd3004e74dc61bb57a680a51f6d62a8062df6a61fc60488ff2f5fb3dee2ac025 | C++ | 25,934 | 670 | #include "ModBaseModel.h"
#include "config/ModBaseModelConfig.h"
#include "nn/ConvStack.h"
#include "nn/LSTMStack.h"
#include "nn/LinearUpsample.h"
#include "nn/WorkingMemory.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/module_utils.h"
#include "torch_utils/tensor_utils.h"
#include "utils/dev_utils.... |
d9dd23dc8fa080139ff25356124d0c1cda15d4550fb6c95ed82efade9df52c11 | C++ | 26,307 | 653 | //
// Created by berry on 2020-07-14.
//
#include <fstream>
#include "processStLFR.h"
#include "read_filter.h"
#define READBUF 1000
processStLFR::processStLFR(C_global_parameter m_gp) : peProcess(m_gp) {
/*set<string> barcodeList;
vector<int> barcodeStartPos;
vector<int> barcodeLength;*/
ifstream bl(m_gp.b... |
ca4244f654857e5606cc8ffb66e9755b8d6a4834051bb1c2d7ecc7ef9bb71da0 | C++ | 26,311 | 798 | #include "secondary/features/encoder_utils.h"
#include <ATen/ATen.h>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <torch/torch.h>
#include <cstdint>
#include <string>
#include <vector>
#define TEST_GROUP "[SecondaryEncoderUtils]"
namespace dorado::secondary::tes... |
cfa62bbe112e942e70a74761e6968bdff880e6d30a92fcb89ae612ab8067bf4d | C++ | 26,351 | 669 | #include "config/BasecallModelConfig.h"
#include "models/kits.h"
#include "models/models.h"
#include <spdlog/spdlog.h>
#include <toml.hpp>
#include <cstddef>
#include <optional>
#include <set>
#include <sstream>
#include <stdexcept>
#include <string>
#include <vector>
namespace {
// the mean Q-score of short reads... |
f9e197ec04cbc7ba32008de33c415875035186ee3b1a51b81204cdc9b60dc018 | C++ | 26,670 | 565 | #include "nn/MetalModules.h"
#include "utils/math_utils.h"
#include <spdlog/spdlog.h>
#include <stdexcept>
#include <string>
#include <vector>
// Splitting up command buffers can be useful since it allows Xcode to make GPU captures.
#define USE_SPLIT_LSTM_COMMAND_BUFFERS 0
namespace {
constexpr int kLstmGates = 4;... |
b6a2eacb9fe38d44e431e585db8fbd00adbaa3f6d6d94fcfec023b4f6818fa6a | C++ | 27,116 | 677 | #include "secondary/features/medaka_read_matrix.h"
#include "hts_utils/bam_utils.h"
#include "local_haplotagging.h"
#include "medaka_bamiter.h"
#include "secondary/common/bam_file.h"
#include "secondary/features/kadayashi_utils.h"
#include "torch_utils/gpu_profiling.h"
#include <htslib/faidx.h>
#include <htslib/khash... |
d40ffb2c5a757fa9f7b2a96bcaf712070672a09cef823d82983eeb084082b20b | C++ | 27,431 | 621 | #include "read_pipeline/nodes/ModBaseCallerNode.h"
#include "config/ModBaseModelConfig.h"
#include "modbase/ModBaseContext.h"
#include "modbase/ModBaseEncoder.h"
#include "modbase/ModBaseRunner.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/m... |
90cc200a4743f282d8a33126f2b5c7c6dd77efaeb867f7f7cbfa61117d415e7e | C++ | 27,447 | 605 | #include "modbase/ModBaseEncoder.h"
#include "modbase/encode_kmer.h"
#include "read_pipeline/nodes/ModBaseChunkCallerNode.h"
#include "utils/sequence_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <s... |
8f1f512968bb8991c36ccf01d8ef4dea64fe1388f329a5268f20e9211929925e | C++ | 27,631 | 627 | #include "model_slot_attention_consensus.h"
#include "torch_utils/tensor_utils.h"
#include <spdlog/spdlog.h>
#include <cmath>
#include <random>
#include <stdexcept>
#include <tuple>
namespace dorado::secondary {
// Keeping the old quick_phase approach for now.
constexpr bool USE_BATCH_ADJACENCY_PHASE = true;
Slot... |
80868413877e26a264924263aa3def5ea4fa68877e72aadbf8d5420dad1af07e | C++ | 27,803 | 608 | #include "beam_search.h"
#include "utils/simd.h"
#include <c10/core/ScalarType.h>
#include <c10/util/Half.h>
#include <math.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <array>
#include <bitset>
#include <cstring>
#include <iostream>
#include <limits>
#include <numeric>
namespace {
// 16 bit state s... |
96d031bad94b6dfb4d3163b2b6a57cd5b363af2bcf71f6dc1bb07fc3a42e7cdd | C++ | 27,897 | 635 | #include "secondary/common/region.h"
#include "secondary/consensus/sample.h"
#include "secondary/consensus/sample_trimming.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <cstdint>
#include <optional>
#include <vector>
namespace dorado::secondary::tests {
#defin... |
9dfdaa5233255e10443662ef9549b18e3c668c6f7651767724837e73b7bd3ed3 | C++ | 28,187 | 691 | #include "secondary/consensus/sample.h"
#include "secondary/common/interval.h"
#include "torch_utils/tensor_utils.h"
#include <ATen/ATen.h>
#include <ATen/TensorIndexing.h>
#include <spdlog/spdlog.h>
#include <ostream>
#include <span>
#include <stdexcept>
namespace dorado::secondary {
void Sample::validate() const... |
6e2d7858c2c39cbb08955e127c2d1979805667fdcfc6187b9dd910a8de14db88 | C++ | 28,245 | 654 | #include "data_loader/DataLoader.h"
#include "models/kits.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/PostCondition.h"
#include "utils/fs_utils.h"
#include "utils/thread_utils.h"
#include "utils/time_utils.h"
#include "utils/types.h"
#include <A... |
56352c883bc94831de607f4367fbd4fd59676ba6a494bca7438684a585362abd | C++ | 28,704 | 656 | #include "read_pipeline/nodes/BasecallerNode.h"
#include "basecall/ModelRunnerBase.h"
#include "config/BasecallModelConfig.h"
#include "read_pipeline/base/chunk.h"
#include "read_pipeline/base/messages/ReadCommon.h"
#include "read_pipeline/base/read_utils.h"
#include "read_pipeline/base/stitch.h"
#include "utils/stats... |
9485072029a0f3cf55cbc44cc3760a844ec33b19c338c980790d7ac02918ee56 | C++ | 29,345 | 798 | #include "torch_utils/gpu_monitor.h"
#include "utils/sys_utils.h"
#if defined(_WIN32) || defined(__linux__)
#define HAS_NVML 1
#else
#define HAS_NVML 0
#endif
#if HAS_NVML
#include "utils/scoped_trace_log.h"
#include "utils/string_utils.h"
#include <nvml.h>
#if defined(_WIN32)
#include <Windows.h>
#else // _WIN32
... |
13e8a88e4aecda1dcb44eb58e2d8aa30dec76b7202e10f680dd1f6419710200e | C++ | 30,424 | 697 | #include "splitter/DuplexReadSplitter.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "splitter/myers.h"
#include "splitter_utils.h"
#include "utils/PostCondition.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include "utils/uuid_utils.h"
#include <ATen/TensorIndexing.h>
#include ... |
139a1cf71b39e6a2ea3e68dfbf1d851e3c75152477b35bbf1566cacf1f7a283e | C++ | 31,005 | 1,088 | #include <string>
#include <vector>
#include <iostream>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <map>
#include "read_filter.h"
#include "global_parameter.h"
#include "gc.h"
using namespace::std;
#define MAX_LENGTH 1000
bool check_tile_or_fov(string tile,string& tile_parameter){
if(tile_pa... |
ac86e40ddab353927de3ddf7f41bd86d411950755dbcfc28319392863b282e02 | C++ | 31,893 | 736 | #include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "aligner/Minimap2Aligner.h"
#include "alignment/alignment_info.h"
#include "alignment/minimap2_args.h"
#include "alignment/minimap2_wrappers.h"
#include "hts_utils/KString.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/header_sq_record.h"
#include "... |
1f3be22e657369261d7b583a852c3bd01a3218f29d6f0b59f2cb733fd4ef3e40 | C++ | 33,285 | 696 | #include "ProgressTracker.h"
#include "alignment/minimap2_args.h"
#include "api/pipeline_creation.h"
#include "api/runner_creation.h"
#include "basecall_output_args.h"
#include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "config/BasecallModelConfig.h"
#include "config/ModBaseBatchParams.h"
#include "config/Mo... |
1222cf8fd4ff14cc960df3c47e24747cfc8ab3596b056c3f966f4a436943ffc8 | C++ | 34,410 | 823 | #include "TestUtils.h"
#include "hts_utils/header_utils.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "hts_writer/HtsFileWriter.h"
#include "hts_writer/HtsFileWriterBuilder.h"
#include "hts_writer/StreamHtsFileWriter.h"
#include "hts_writer/Structure.h"
#include "utils/PostCondition.h"
#i... |
ecea6a2e2ff0e7d5af5509369b7e4579bcf960f7b7797e0ec2b4fb87630e1116 | C++ | 34,777 | 823 | #include "cli.h"
#include "haplotag_lib/string_utils.h"
#include "ketopt.h"
#include "resources.h"
#include <spdlog/spdlog.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <cstdio>
#include <cstdlib>
ketopt_t opt;
// clang-format off
static ko_longopt_t longopts[] = {
{"vcf", ko_required_argument, ... |
48ad0f402c86d2da962971bcdf6ca778aa6149ee2af38bf3ec867f8a617ca84f | C++ | 35,025 | 798 | #include "secondary/consensus/sample.h"
#include <catch2/catch_test_macros.hpp>
#include <torch/torch.h>
#include <cstdint>
#include <ostream>
#include <utility>
#include <vector>
namespace dorado::secondary {
template <typename T>
std::ostream& operator<<(std::ostream& os, const IntervalGeneric<T>& interval) {
... |
e7e4d11dfc33f1f4350fa3e3841f31da882cc4d4b4d072cb5c78c1d9f194c94d | C++ | 35,302 | 762 | #include "basecall/CudaCaller.h"
#include "ChunkBenchmarks.h"
#include "basecall/crf_utils.h"
#include "decode/Decoder.h"
#include "torch_utils/cuda_utils.h"
#include "utils/math_utils.h"
#include "utils/memory_utils.h"
#include "utils/sys_utils.h"
#include "utils/thread_utils.h"
#include <ATen/cuda/CUDAContext.h>
#i... |
98b1eb1d79edd601c70be01be00381ccf519c93b7f40c972b7ce4ebcf2e26806 | C++ | 35,964 | 832 | #include "correct/windows.h"
#include "correct/conversions.h"
#include "correct/features.h"
#include "correct/types.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h"
#include "torch_utils/gpu_profiling.h"
#include "utils/paf_utils.h"
#include <spdlog/spdlog.h>
#include <functional>
#include <sstream>
... |
ed0f7013344efbf5536ea65689bb0374ec5504c6d7238c690502676dad20393b | C++ | 36,200 | 677 | #include "demux/AdapterDetector.h"
#include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "demux/Trimmer.h"
#include "demux/adapter_info.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/messages/ReadPair.... |
3546c6b2c557dc850e0d1bcd04f7485788c19b50a3909992881c63e3c486b1eb | C++ | 37,528 | 821 | #include "secondary/common/variant.h"
#include "secondary/consensus/variant_calling.h"
#include "secondary/consensus/variant_calling_sample.h"
#include "secondary/features/decoder_base.h"
#include "torch_utils/tensor_utils.h"
#include <ATen/ATen.h>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/ca... |
9e73e81b38c6b6e36a17566a8dfc16e2da2e54fab44dfdbcb85485d77998b701 | C++ | 41,435 | 960 | #include "nn/TxModules.h"
#include "config/BasecallModelConfig.h"
#include "nn/TxModules.h"
#include "torch_utils/gpu_profiling.h"
#include "utils/dev_utils.h"
#include "utils/math_utils.h"
#include <ATen/TensorIndexing.h>
#include <ATen/ops/scaled_dot_product_attention.h>
#include <c10/core/ScalarType.h>
#include <c... |
6f324d4a04f5e90a463bfd7ea4742c09b5a5dd71853fca571550d5b02638e7ea | C++ | 46,543 | 1,234 | #include "variant_graph.h"
#include "sequence_utility.h"
#include <spdlog/fmt/bundled/format.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <array>
#include <cstdio>
#ifdef NDEBUG
#define LOG_TRACE(...)
#define LOG_DEBUG(...)
#else
#define LOG_TRACE(...) spdlog::trace(__VA_ARGS__)
#define LOG_DEBUG(...... |
77ddd44a75093bca8c56f9fa461b8565da1c3130d01ac3946a2b6f64ecacc6fa | C++ | 53,439 | 1,373 | #include "secondary/consensus/variant_calling.h"
#include "secondary/consensus/consensus_result.h"
#include "secondary/consensus/consensus_utils.h"
#include "torch_utils/tensor_utils.h"
#include "utils/rle.h"
#include "utils/sequence_utils.h"
#include <ATen/ATen.h>
#include <cxxpool.h>
#include <spdlog/spdlog.h>
#in... |
33ef3b531810a538f9131239c3b2a0114a1a212956ce658b6b39ef6afb391764 | C++ | 53,669 | 1,206 | #include "ProgressTracker.h"
#include "alignment/minimap2_args.h"
#include "api/pipeline_creation.h"
#include "api/runner_creation.h"
#include "basecall_output_args.h"
#include "batchsize_benchmarks/batchsize_benchmarks.h"
#include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "config/BasecallModelConfig.h"
#in... |
a865ff1ce1ea323c45dc05aa691f2d83211c5c333fb5daa6a3c71066fa7199a2 | C++ | 53,870 | 1,243 | #include "read_pipeline/nodes/ModBaseChunkCallerNode.h"
#include "config/ModBaseModelConfig.h"
#include "modbase/ModBaseContext.h"
#include "modbase/encode_kmer.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/dev_utils.h"
#include "utils/math_... |
d646a1748b6b23a0f73464a570e307b67f051549dd14d19604cc1a0372f548d6 | C++ | 53,900 | 1,638 | #include "process_argv.h"
#include <stdlib.h>
#include <iostream>
#include <stdio.h>
#include <getopt.h>
#include <map>
#include <fstream>
#include "global_parameter.h"
#include "sys/sysinfo.h"
// #include <string>
using namespace ::std;
#define ADA_RATIO 0.4
map<string, vector<string>> wrong_paras;
void check_module... |
dcccdb9d62258161bc19cd8eb009404b19c646d80511c69dc5d5d3bf0a7f1690 | C++ | 55,887 | 1,157 | #include "secondary/architectures/model_factory.h"
#include <catch2/catch_test_macros.hpp>
// Need to include implementation details to perform dynamic_cast<>s in tests.
#include "../model_gru.h"
#include "../model_latent_space_lstm.h"
#include "../model_slot_attention_consensus.h"
#include "../model_variant_perceive... |
56b01484ad958e9a078fb3d99a0adcee651e4017d2cf4c87626807f3d41eb116 | C++ | 58,413 | 1,257 | #include "model_variant_perceiver.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include <spdlog/spdlog.h>
#include <cmath>
#include <cstdint>
#include <random>
#include <stdexcept>
#include <tuple>
// #define DEBUG_VARIANT_PERCEIVER_DATA_TYPES
#ifdef NDEBUG
#define LOG_TRACE(...)... |
63b002cec63a77376f625f5e8f609b7b9085ff5917a1bcd36c8b6821c291331b | C++ | 59,114 | 1,331 | #include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "dorado_version.h"
#include "hts_utils/FastxRandomReader.h"
#include "hts_utils/fai_utils.h"
#include "model_downloader/model_downloader.h"
#include "model_resolver/ModelResolver.h"
#include "models/models.h"
#include "polish/polish_impl.h"
#include "polish... |
d5fe04239898af8b3b1fa278885e6fd3c784ea6d4f50084233b5f5a61b98e6cb | C++ | 65,057 | 2,212 | // [[Rcpp::depends(RcppEigen)]]
// [[Rcpp::interfaces(r,cpp)]]
#include <RcppEigen.h>
#include <Rcpp.h>
using namespace Rcpp;
//typedef Eigen::SparseMatrix<double> SpMat;
//typedef Eigen::SparseMatrix<double>::InnerIterator InIterMat;
/***** Center and standardize *****/
// [[Rcpp::export]]
List scaleC(Eigen::Matr... |
330dd0f99bf9d42a31e10991415fd66d2610dd3f65806c63a0f193147a445ba7 | C++ | 66,963 | 1,101 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include "../inst/include/Scissor.h"
#include <RcppEigen.h>
#include <Rcpp.h>
#include <string>
#include <set>
using namespace Rcpp;
// scaleC
List scaleC(Eigen::MatrixXd X);
static SEXP _S... |
9cdd8ed3827ff4686a5315cc5c2fe4d7f3fbbbf4a6bcbcab161d38baf4104243 | C++ | 68,901 | 1,517 | #include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "dorado_version.h"
#include "hts_utils/FastxRandomReader.h"
#include "hts_utils/fai_utils.h"
#include "model_downloader/model_downloader.h"
#include "model_resolver/ModelResolver.h"
#include "models/models.h"
#include "secondary/architectures/model_config.h... |
b949f34bb31bf45fc2fa356efa51cee57545bd4c52292208cfc3d004186370ed | C++ | 74,495 | 1,635 | #include "TestUtils.h"
#include "blocked_bloom_filter.h"
#include "hts_utils/FastxRandomReader.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "local_haplotagging.h"
#include "secondary/common/bam_file.h"
#include "secondary/features/medaka_read_matrix.h"
#include "sequence_utility.h"
#incl... |
064055cf4e41365f440b142acf8945f1500a55f74a2995cc0b4895d3bf89031a | C++ | 78,074 | 1,861 | #include "utils/barcode_kits.h"
#include <algorithm>
#include <numeric>
#include <set>
#include <stdexcept>
namespace dorado::barcode_kits {
namespace {
inline const std::string UNCLASSIFIED = "unclassified";
// Flank sequences per barcode kit.
// There are 2 types of kits described here -
// 1. Double ended kits ... |
a0f9a3cb93557f4bf247cb6c6590e209a85dde1d37fd7c961eac5ff8edc4e41d | C++ | 78,880 | 1,844 | #include "../dorado/secondary/features/encoder_read_alignment.h"
#include "TestUtils.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "secondary/features/encoder_utils.h"
#include "secondary/features/haplotag_source.h"
#include "secondary/features/kadayashi_options.h"
#include "utils/cigar.h... |
12c297176a7c715cc68277945ae825c1aad991484ec3023e86cd02600681825a | C++ | 80,060 | 1,602 | #include "demux/BarcodeClassifier.h"
#include "utils/alignment_utils.h"
#include "utils/barcode_kits.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include "utils/types.h"
#include <edlib.h>
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <stdexcept>
#include <str... |
f2d12e1168e140d63ed3bd0d6693fd5a994856967a33351e07af6cb37e7dd4bc | C++ | 81,188 | 2,297 | //
// Created by berry on 2020-04-08.
//
#include "processHts.h"
#define bam_is_read1(b) (((b)->core.flag&BAM_FREAD1)!=0)
#define bam_is_read2(b) (((b)->core.flag&BAM_FREAD2)!=0)
#define BAMCPERR "bam copy error"
//if MultiThreadsMethod is set to 1, IO independent
//if is set to 2, IO is locked
#define MultiThreadsMeth... |
4152496befe53c3ff6143205d2aa717a94fe003d26e3d6988f6b6eca108c5c0e | C++ | 82,832 | 1,823 | #include "polish/polish_impl.h"
#include "hts_utils/FastxRandomReader.h"
#include "secondary/architectures/model_factory.h"
#include "secondary/common/batching.h"
#include "secondary/common/region.h"
#include "secondary/consensus/sample_collate_utils.h"
#include "secondary/consensus/variant_calling.h"
#include "second... |
9a74b14a48336f5dd5d7afe472612e8d0561e3d13f5c4c93d8e83096a74fab0b | C++ | 83,000 | 2,744 | #include <iostream>
#include <string>
#include <stdlib.h>
#include <limits.h>
#include <string.h>
#include <thread>
#include <mutex>
#include <fstream>
#include <iomanip>
#include <dirent.h>
#include <fcntl.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <sys/mman.h>
#include <math.h>
#include "seprocess.h"
#i... |
db16f7808d92aaf8bdddcc030cb1d803d52574c6555c291562e17dae4b101f60 | C++ | 95,073 | 2,205 | #include "variant/variant_impl.h"
#include "hts_utils/FastxRandomReader.h"
#include "secondary/architectures/model_factory.h"
#include "secondary/common/batching.h"
#include "secondary/common/region.h"
#include "secondary/consensus/sample_collate_utils.h"
#include "secondary/consensus/variant_calling.h"
#include "seco... |
a6ab5692a5c17a8142df586cb61f89748130cd963530c0abbfb21a47e1dc4645 | C++ | 95,476 | 2,414 | #include "pipeline.h"
#include "bam_record_parsing.h"
#include "bam_tagging.h"
#include "haplotag_lib/string_utils.h"
#include "haplotag_lib/variant_graph.h"
#include "hts_utils/FastxRandomReader.h"
#include "kadayashi_utils.h"
#include "resources.h"
#include "sequence_utility.h"
#include "types.h"
#include <cxxpool.... |
b2e99e9d7ee2218c55f26610733aea2ba0d1ba6efb0e59004bc1b38bdd0da5eb | C++ | 97,635 | 2,211 | #include "TestUtils.h"
#include "hts_utils/fai_utils.h"
#include "secondary/architectures/model_torch_base.h"
#include "secondary/features/decoder_base.h"
#include "variant/variant_impl.h"
#include <ATen/ATen.h>
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_string.hpp>
#include <alg... |
fc62fc9485f90f30ad7cdc327a295b089e332855227cad3d0ab25e65c2f7cd9d | C++ | 99,665 | 2,323 | #include "models/models.h"
#include "models/kits.h"
#include "models/metadata.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cstddef>
#include <exception>
#include <filesystem>
#include <iterator>
#include <optional>
#include <stdexcept>
#include <string>
#include <string_view>
#include <unordered_map>... |
05324b1a735a0a93e8db9784cebd05e8f25820b31f1b8315101ad2da328a6729 | C++ | 133,010 | 3,807 | #include <iostream>
#include <string>
#include <stdlib.h>
#include <limits.h>
#include <string.h>
#include <thread>
#include <mutex>
#include <fstream>
#include <iomanip>
#include <sstream>
#include <time.h>
#include <dirent.h>
#include <math.h>
#include <unistd.h>
#include <string.h>
#include "peprocess.h"
#include "p... |
078673c9dbacdf6ed8d46eb0875378f6118b9356e66993065375f064e2914038 | C++ | 142,214 | 4,629 | /*******************************************************************************
* *
* Author : Angus Johnson *
* Version : 6.4.2 ... |
b1234fa3eddd44f885e05ea6ed8255808b2ce5a84321cbd4c54e04f1f4492aa0 | C++ | 169,210 | 3,895 | #include "local_haplotagging.h"
#include "bam_record_parsing.h"
#include "blocked_bloom_filter.h"
#include "faidx_utils.h"
#include "hts_types.h"
#include "hts_utils/bam_utils.h"
#include "sequence_utility.h"
#include "string_utils.h"
#include "variant_graph.h"
#include <htslib/bgzf.h>
#include <htslib/faidx.h>
#incl... |
08d323ea75beb9df1e90c0af1a5fa56d1a104536a0fa194d855ac5b20446c5fa | C/C++ | 22 | 1 | #define CUDNN_MAJOR 8
|
1305d054c47e1ee8a5390ccb1c8c844e02cc3035934e700958d32270998f1a22 | C/C++ | 23 | 1 | #include <ATen/ATen.h>
|
e9cea210bfc93ad77e15bcd12360f6a240a91f2e20700a2fe0283cbbb63f2f05 | C/C++ | 98 | 7 | #pragma once
namespace dorado::utils {
bool running_in_docker();
} // namespace dorado::utils
|
c848b780b85ded2f28949078b26569f9f16e3ab00be2d426a1bee7261136b732 | C/C++ | 107 | 10 | #pragma once
namespace dorado::utils::concurrency {
enum class TaskPriority {
normal,
high,
};
} |
71c4c9b7859c23e2733b5cd3e6b4d17e876551d9525edc722fce5c15c3b2dc5e | C/C++ | 162 | 11 | #pragma once
namespace kadayashi {
double get_timestamp();
double get_peakrss();
extern bool KDY_VERBOSE; // verbosity used by CLI
} // namespace kadayashi |
13795f662197e5f7dcd29318d3be5aebcd99560325c450db9484832f95312eb8 | C/C++ | 170 | 6 | #ifndef LZWENCODE_H
#define LZWENCODE_H
#include <stdint.h>
#include "tiffio.h"
uint64_t lzwEncode(uint8_t* unCompr, uint8_t* compr, tmsize_t len);
#endif // LZWENCODE_H
|
08b887ebcb11229839b0686da1d32fa13908f69ee32142f928af894d595c1351 | C/C++ | 178 | 14 | #ifndef CONFIGPARAM_H
#define CONFIGPARAM_H
class ConfigParam
{
public:
ConfigParam();
float *data;
int row;
int col;
};
#endif // CONFIGPARAM_H
|
f0a25acab28d5a377a3bfa3c8c670b42bca4736fd3943e592efc61803dfc3742 | C/C++ | 185 | 7 | #include <optional>
#include <string>
#include <unordered_set>
namespace dorado::utils {
std::optional<std::unordered_set<std::string>> load_read_list(const std::string& read_list);
}
|
d4a307df064fd9e306dc630d7fcd8a6057ba4f4931c47813af46896309a45137 | C/C++ | 187 | 7 | #pragma once
namespace dorado::utils {
// Ensures std::setlocale(LC_ALL, "") will succeed.
// See DOR-234 for details.
void ensure_user_locale_may_be_set();
} // namespace dorado::utils |
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