sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f8fd6b47c9b016b1c78c6e1532bb307074395a3b6d4ad933b3c932d5c3f3007c | C++ | 823 | 28 | #include "utils/scoped_trace_log.h"
#include <spdlog/spdlog.h>
namespace dorado::utils {
namespace {
const std::string SCOPED_LOG_ENTER{"[ENTRY]"};
const std::string SCOPED_LOG_EXIT{"[EXIT]"};
const std::string SCOPED_LOG_MESSAGE{"[MSG]"};
} // namespace
ScopedTraceLog::ScopedTraceLog(std::string context) : m_cont... |
770eedae2612a55c1ce9cfd84eb8cc64b92ec03dd029d5afe5c751cfd316f693 | C++ | 833 | 32 | #include "resources.h"
#if defined(__linux__) || defined(__unix__) || defined(__APPLE__) || defined(_POSIX_VERSION)
#include <sys/resource.h>
#endif
#include <chrono>
#include <cstddef>
#include <cstdlib>
namespace kadayashi {
bool KDY_VERBOSE = false;
double get_timestamp() {
return static_cast<double>(std::c... |
8450b4442e9c62f6c12786c06cfdd4a809577337e531150388954144d7a4020b | C++ | 899 | 33 |
#include "torch_utils/torch_utils.h"
#include "utils/locale_utils.h"
#include <catch2/catch_session.hpp>
#include <catch2/catch_test_macros.hpp>
#include <nvtx3/nvtx3.hpp>
#include <torch/utils.h>
int main(int argc, char* argv[]) {
// global setup...
dorado::utils::ensure_user_locale_may_be_set();
dora... |
e9afcff2a358d8f340c8c117de89c0c93248cc67c1d26fdd8d93694ba5d3313f | C++ | 905 | 28 | #include "utils/dev_utils.h"
namespace dorado::utils::details {
std::unordered_map<std::string, std::pair<double, bool>> g_dev_options;
void extract_dev_options(const std::string& env_string) {
constexpr char SEPARATOR = ';';
std::vector<std::string> parts;
size_t start = 0;
for (size_t end = env_str... |
3c61f87363d525d5b2c7848187bdb3b8dfb0b99b2c619c9ad73991fff9131084 | C++ | 928 | 28 | #include "secondary/common/window.h"
#include <ostream>
#include <sstream>
#include <tuple>
namespace dorado::secondary {
std::ostream& operator<<(std::ostream& os, const Window& w) {
os << "seq_id = " << w.seq_id << ", seq_length = " << w.seq_length << ", start = " << w.start
<< ", end = " << w.end << ",... |
7721617383aa134dfa37378fa836c22c56d9d233e2b137176246a64dd82c4613 | C++ | 928 | 28 | #include "resume_loader/ResumeLoader.h"
#include "MessageSinkUtils.h"
#include "TestUtils.h"
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[resume_loader][ResumeLoader]"
namespace fs = std::filesystem;
CATCH_TEST_CASE(TEST_GROUP) {
std::vector<dorado::Message> messages;
MessageSinkToVector si... |
e31fcb8813c47ee7da7377cd55bac1db13ed6eb7865e1f89647d54098f6b9daa | C++ | 930 | 42 | #include "hts_utils/KString.h"
#include <htslib/sam.h>
#include <memory>
namespace dorado {
KString::KString() : m_data(std::make_unique<kstring_t>()) { *m_data = {0, 0, nullptr}; }
KString::KString(size_t n) : m_data(std::make_unique<kstring_t>()) {
*m_data = {0, 0, nullptr};
ks_resize(m_data.get(), n);
}... |
2efb2655525aa7e1c746e269a41b39188d490079b0e7b79e7f91d38939a9255e | C++ | 1,023 | 34 | #include "api/caller_creation.h"
#if DORADO_CUDA_BUILD
#include "basecall/CudaCaller.h"
#include "config/BatchParams.h"
#elif DORADO_METAL_BUILD
#include "basecall/MetalCaller.h"
#endif
#include "modbase/ModBaseCaller.h"
namespace dorado::api {
#if DORADO_CUDA_BUILD
std::shared_ptr<basecall::CudaCaller> create_cuda... |
3c4dec4814567e94fcc7b1d430fcd23cf20110fe74fea0fecdba087ee02e4bd9 | C++ | 1,044 | 33 | #include "read_pipeline/nodes/ReadForwarderNode.h"
namespace dorado {
void ReadForwarderNode::input_thread_fn() {
Message message;
while (get_input_message(message)) {
if (is_read_message(message)) {
m_message_callback(std::move(message));
}
}
}
ReadForwarderNode::ReadForwarde... |
26fe0adc820b2744aedae15d46ae0c6684cfc7fc0dc2325ac67c031fe206bad3 | C++ | 1,062 | 39 | #include "compat/compat_utils.h"
// For some reason AppleClang 2100.0.123.102 confuses ninja when this file is compiled, leading
// to it being rebuilt and hence relinked into everything. Presumably this is because it's
// completely empty after preprocessing. Adding this comment "fixes" the issue.
#ifdef _WIN32
#de... |
0472a10301eb841f1d9e9caafbff23a8a5f83e78d0e05c5302c5f77f27ff3ad1 | C++ | 1,136 | 40 | #include "utils/benchmark_timer.h"
#include "utils/thread_utils.h"
namespace dorado {
BenchmarkTimer::BenchmarkTimer(std::chrono::seconds benchmarking_period, ShutdownCallback callback)
: m_shutdown_callback(std::move(callback)),
m_benchmarking_thread(
[this, benchmarking_period] ... |
12c2b05c314ba8d8f355f36f0a5806db2ad4642c028bbf82982bc10d253f012c | C++ | 1,145 | 30 | #include "demux/KitInfoProvider.h"
#include "utils/barcode_kits.h"
#include <stdexcept>
namespace dorado::demux {
KitInfoProvider::KitInfoProvider(const std::string& kit_name) : m_kit_names({kit_name}) {}
const barcode_kits::KitInfo& KitInfoProvider::get_kit_info(const std::string& kit_name) const {
const auto... |
edef6abe61646abb2bc7b258fa6ecd910dad03373db6c818cc4087d46675d35d | C++ | 1,166 | 44 | #include "sequence_utility.h"
#include <algorithm>
#include <cstdint>
namespace kadayashi {
std::vector<uint8_t> seq2nt4seq(const std::string_view &seq) {
std::vector<uint8_t> h;
h.reserve(seq.size());
for (size_t i = 0; i < seq.size(); i++) {
h.emplace_back(
static_cast<uint8_t>(... |
b64b171a8af75748aca652b9e9a1c87ea7f03a9d354747cdc2688cc661269701 | C++ | 1,179 | 43 | #include "correct/conversions.h"
#include <array>
#include <string>
namespace dorado::correction {
float normalize_quals(float q) { return 2.f * (q - MIN_QSCORE) / (MAX_QSCORE - MIN_QSCORE) - 1.f; }
std::array<char, 128> base_forward_mapping() {
std::array<char, 128> base_forward = {0};
base_forward['*'] = ... |
36f849d2873ae819a8e3eed3e47f286fb5f60f1550d4e226e0afaacbdf7c677b | C++ | 1,181 | 38 | #include "utils/uuid_utils.h"
#include "utils/crypto_utils.h"
#include <algorithm>
#include <array>
#include <iomanip>
#include <sstream>
namespace dorado::utils {
std::string derive_uuid(const std::string& input_uuid, const std::string& desc) {
// Hash the input UUID+desc using SHA-256
const auto hash = ut... |
6572285e1915dce4c7648747442e993bceace9931877613ca0e29bd3504094f4 | C++ | 1,213 | 33 | #include "secondary/common/alignment.h"
#include <ostream>
#include <sstream>
namespace dorado::secondary {
void serialize_alignment(std::ostream& os,
const Alignment& aln,
const std::string_view separator,
const bool write_cigar) {
os <<... |
08958d0b51e21dadc179f7c3d75b53638f5676e7726b1a35ba204532da889a1b | C++ | 1,217 | 46 | void mexmetypecheck(const mxArray *arr,int expected,char *errorMsg)
{
int thetype = mxGetClassID(arr);
char passed = 0;
if(expected == mxINT8_CLASS ||
expected == mxINT16_CLASS ||
expected == mxINT32_CLASS ||
expected == mxINT64_CLASS)
{
if(thetype == mxINT8_CLASS ||
... |
2d2cc48670ec11a2c581c21d8a1b769bd6e5a216981530eb3f0e4a7438b24c58 | C++ | 1,242 | 44 | #include "utils/container_utils.h"
#include <algorithm>
#include <sstream>
#include <unordered_set>
namespace dorado::utils {
std::vector<int32_t> parse_int32_vector(const std::string& input, const char delimiter) {
if (std::empty(input)) {
return {};
}
const std::unordered_set<char> open_set{'(... |
f35c29864aae8ce034c250c8fe3c493ca794b2f0cf824a5d050e3f27f3d9dbca | C++ | 1,293 | 31 | #include "read_pipeline/nodes/ReadForwarderNode.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/ReadPair.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[ReadF... |
d2cfa94229ec1c5cfeabc901532bdd9a7386719326a1b91fde945bb534021bcf | C++ | 1,298 | 43 | #include "utils/PostCondition.h"
#include <catch2/catch_test_macros.hpp>
#define CUT_TAG "[PostCondition]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
using dorado::utils::PostCondition;
DEFINE_TEST("Condition isn't triggered right away") {
int counter = 0;
auto on_scope_end = PostC... |
23578a357137de3a04619fb0cd963c58b77cfec53c5a8399cae15df3c9378296 | C++ | 1,304 | 52 | #include "utils/alignment_utils.h"
#include <minimap.h>
namespace dorado::utils {
std::string alignment_to_str(const char* query,
const char* target,
const EdlibAlignResult& result) {
std::string ss;
ss.reserve(result.alignmentLength * 3 + 2);
in... |
9f8ae183210f552692cad2b940cb7c659914f854ed9da50602b5cd989f22802f | C++ | 1,307 | 43 | #include "nn/KoiUtils.h"
#include <ATen/cuda/CUDAContext.h>
namespace {
bool koi_can_use_cutlass_internal(const cudaDeviceProp *const prop) { return (prop->major >= 8); }
bool koi_can_run_flstm_internal(const cudaDeviceProp *const prop) {
return (prop->major >= 8) && (prop->multiProcessorCount >= 9);
}
} // n... |
12a86ebcd0f61d2610e7e3e79e4a144c72b0a97daa1139e0c66125a8f6d3fd46 | C++ | 1,348 | 38 | #include "demux/parse_custom_sequences.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/HtsReader.h"
#include <htslib/sam.h>
namespace dorado::demux {
std::vector<CustomSequence> parse_custom_sequences(const std::string& sequences_file) {
const std::size_t num_threads = 1;
HtsReader reader(s... |
d564f97fb6058aae5ee0996dfd87712140846235f84320d1344999c1211aea39 | C++ | 1,353 | 33 | #include "read_pipeline/nodes/ReadToBamTypeNode.h"
#include "MessageSinkUtils.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <catch2/catch_test_macros.hpp>
#include <memory>
#include <vector>
#define TEST_GROUP "[ReadToBamTypeNodeTest]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(TEST_GROUP " " name... |
b3a547df5fcb4594a0fcfee0c5dd043f6aeb9a24693f69c796fcd1d719074a61 | C++ | 1,358 | 43 | #include "utils/sys_stats.h"
#ifdef __linux__
#include <sys/resource.h>
#elif __APPLE__
#include <mach/mach_init.h>
#include <mach/task.h>
#include <sys/sysctl.h>
#endif
namespace dorado {
namespace stats {
ReportedStats sys_stats_report() {
stats::NamedStats named_stats;
#ifdef __linux__
rusage usage;
c... |
7d78ed19f74464e70cc0183fcdd693572786a3b83dd47516ba908f059c3f3465 | C++ | 1,411 | 43 | #include "read_pipeline/nodes/CorrectionPafWriterNode.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h"
#include "utils/paf_utils.h"
#include <iostream>
namespace dorado {
CorrectionPafWriterNode::CorrectionPafWriterNode() : MessageSink(10000, 1) {}
CorrectionPafWriterNode::~CorrectionPafWriterNode(... |
c03985a3ed94900f19b5ba2f5f475d8982c36f3bef3246072320a801482759da | C++ | 1,421 | 54 | #include "statuslightstyle.h"
StatusLightStyle::StatusLightStyle()
{
}
QString StatusLightStyle::getChannelActivationStyle()
{
QString styleDescription ="";
return styleDescription;
}
QString StatusLightStyle::getChannelCloseStyle()
{
QString styleDescription ="";
return ... |
4670b3e8aaa9d98e0a56f5fba51119b7bc2b83435cb7cef82a275f1d87c249b4 | C++ | 1,430 | 40 | #include "hts_utils/sequence_file_format.h"
#include "utils/string_utils.h"
#include <algorithm>
#include <string>
namespace dorado::hts_io {
SequenceFormatType parse_sequence_format(const std::filesystem::path& in_path) {
SequenceFormatType fmt = SequenceFormatType::UNKNOWN;
// Convert the string to lower... |
fb9184a3755819242c820c24cb9c8976022f88e22908fa2097f2f0a4047a20ed | C++ | 1,434 | 50 | #include "TxModel.h"
#include "config/BasecallModelConfig.h"
#include "nn/LinearUpsample.h"
#include "nn/TxModules.h"
#include "torch_utils/gpu_profiling.h"
namespace dorado::basecall::model {
TxModelImpl::TxModelImpl(const config::BasecallModelConfig &config,
const at::TensorOptions &option... |
dcc21711f0141e9e232f4e65e8cad28f9a6e0a47d0896901f3fd7147f73a1f4f | C++ | 1,442 | 36 | #include "MetalCRFModel.h"
#include "torch_utils/module_utils.h"
using namespace dorado::utils;
namespace {
CREATE_POINT_OF_INTEREST_ID(MetalCRFModel);
} // namespace
namespace dorado::basecall::model {
MetalCRFModelImpl::MetalCRFModelImpl(const config::BasecallModelConfig &config,
... |
c4fd7779027da04421c52fa4d6670554d5b2ae20e1e1251b822776d2ee6c01cf | C++ | 1,468 | 61 | //
// Created by berry on 2020-10-19.
//
#include "ReverseBloomFilter.h"
ReverseBloomFilter::ReverseBloomFilter(long readsNum, float multiple) {
arrSize=readsNum*multiple;
arr=new long[arrSize];
}
ReverseBloomFilter::ReverseBloomFilter(long readsNum, float multiple, long memSizeUsedInRmdup) {
arrSize=rea... |
f0978cf8d8a30eb89aa5e3ccf7712a62592cf47dc8ec168e045af17441d9bd46 | C++ | 1,493 | 41 | #include "TestUtils.h"
#include "cli/utils/cli_utils.h"
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[cli_utils]"
using namespace dorado::cli;
CATCH_TEST_CASE("CliUtils: Check thread allocation", TEST_GROUP) {
int aligner_threads, writer_threads;
CATCH_SECTION("fraction > 0") {
std::... |
ffc770f5e89865f605152029d7213b3a9c833eaba3b743a5d57e6bd48c9da9f7 | C++ | 1,500 | 48 |
#include "scrollareastyle.h"
ScrollAreaStyle::ScrollAreaStyle()
{
}
QString ScrollAreaStyle::getChannleSelectScrollAreaStyle(){
QString styleDescription = "scrollArea{\
border: 2px solid #c3c3c3;\
border-radius:5px;\
}\
\
QScrol... |
68785f30e32bd902d9011695e02c2f6973281876c7a7f80cc20b02ea40fb37c3 | C++ | 1,517 | 49 | #include "BenchmarkSink.h"
#include <mutex>
namespace dorado::batchsize_benchmarks {
BenchmarkSink::BenchmarkSink() : MessageSink(1000, 4) {}
BenchmarkSink::~BenchmarkSink() { terminate({.fast = utils::AsyncQueueTerminateFast::Yes}); }
std::string BenchmarkSink::get_name() const { return "BenchmarkSink"; }
void B... |
117a43d70095de60d537173d01308dcc4dee54db7c9316939a1edb84a5c44b1d | C++ | 1,532 | 40 | #include "utils/math_utils.h"
#include <catch2/catch_approx.hpp>
#include <catch2/catch_test_macros.hpp>
#define CUT_TAG "[MathUtils]"
CATCH_TEST_CASE(CUT_TAG ": test quantiles", CUT_TAG) {
std::vector<double> in = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
auto quartiles = dorado::utils::quantiles(in, {0.25, 0.5,... |
b89f84d7db82164cb613efe3d52c7c6906893eff065f34a1a2991ed04ae7f382 | C++ | 1,617 | 62 | #include "utils/cigar.h"
#include <ostream>
#include <sstream>
namespace dorado {
std::ostream& operator<<(std::ostream& os, const CigarOp& a) {
os << a.len << convert_cigar_op_to_char(a.op);
return os;
}
std::string cigar_op_to_string(const CigarOp& a) {
return std::to_string(a.len) + std::string(1, co... |
8f299784f892da29ef74d3c6bb8755e18128503ce298219290eaab32d171bc8f | C++ | 1,622 | 58 | #include "polish_progress_tracker.h"
#include <spdlog/spdlog.h>
#include <algorithm>
namespace dorado::polisher {
PolishProgressTracker::PolishProgressTracker() = default;
PolishProgressTracker::~PolishProgressTracker() = default;
void PolishProgressTracker::set_description(const std::string& desc) {
m_progre... |
1d6b1171fe9d4fb84cfabcb910760cfd5b0911418eef7d246cbd846fe47e1e52 | C++ | 1,669 | 60 | #include "smallvar_progress_tracker.h"
#include "utils/tty_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
namespace dorado::smallvar {
VariantProgressTracker::VariantProgressTracker() = default;
VariantProgressTracker::~VariantProgressTracker() = default;
void VariantProgressTracker::set_description(co... |
59fd35a1a6e1aaf20271f57315f3f2a155ef5583c0b75b4680b180e44e8c1b27 | C++ | 1,672 | 47 | #include "basecall/MetalModelRunner.h"
#include "basecall/MetalCaller.h"
#include <ATen/TensorIndexing.h>
#include <spdlog/spdlog.h>
namespace dorado::basecall {
MetalModelRunner::MetalModelRunner(std::shared_ptr<MetalCaller> caller)
: m_caller(std::move(caller)), m_input(m_caller->create_input_tensor()) {}... |
fa27f4f36b6dec9d9011da5f7981442a8ee2a0e23c460b9aa15c253d3ed1773a | C++ | 1,729 | 44 | #include "utils/locale_utils.h"
#ifndef _WIN32
#include <stdlib.h>
#include <clocale>
#endif
namespace dorado::utils {
void ensure_user_locale_may_be_set() {
// JIRA issue DOR-234.
// The indicators library tries to set the user preferred locale, so we ensure
// this is possible.
#ifdef _WIN32
// No... |
af1447331129b00220f33ba46928be78c82fd72007ef25130cec29dc1e8cdee2 | C++ | 1,791 | 75 | #include "main_widget.h"
#include "controldialog.h"
#include "ui_controldialog.h"
#include "QDebug"
ControlDialog::ControlDialog(QWidget *parent) :
QDialog(parent),
ui(new Ui::ControlDialog)
{
ui->setupUi(this);
setWindowFlag(Qt::WindowStaysOnTopHint,true);
setWindowFlag(Qt::WindowCont... |
ba6e68fb9decd0380da5140b68de6fcd0b59f1ab75eab982716da27673420680 | C++ | 1,805 | 60 | #include "buttonstyle.h"
#include "channelselectlayout.h"
#include <QDebug>
#include <QSignalMapper>
ChannelSelectLayout::ChannelSelectLayout()
{
setContentsMargins(10,0,10,0);
setVerticalSpacing(10); // ÉèÖÃÐмä¾àΪ10ÏñËØ
setHorizontalSpacing(0); // ÉèÖÃÁмä¾àΪ0ÏñËØ
channelSelectList = ... |
db390015449cf36f4e4c1319cd8c555a2ba30aa983382169bc33aaf1b070f618 | C++ | 1,817 | 36 | #include "utils/arg_parse_ext.h"
#include <catch2/catch_test_macros.hpp>
#define CUT_TAG "[dorado::utils::arg_parse]"
namespace dorado::utils::arg_parse::test {
CATCH_TEST_CASE(CUT_TAG " Check number string to long conversion", CUT_TAG) {
CATCH_SECTION("convert #K") { CATCH_CHECK(parse_string_to_size("5K") == 5... |
1ddcf239bad9f58470b08586f21b1d151e6eba40ed82640d8c6e89803a947e3b | C++ | 1,840 | 66 | #include "hts_utils/FastxSequentialReader.h"
#include <htslib/faidx.h>
#include <spdlog/spdlog.h>
#include <zlib.h>
#include <stdexcept>
#include <vector>
#ifdef _MSC_VER
#pragma warning(push)
#pragma warning(disable : 4146) // unary minus on unsigned
#pragma warning(disable : 4244) // conversion from 'int' to 'ch... |
165d59528d96bd49d9114d109e493a062652b78db09b2f2c4d7f444f647247c1 | C++ | 1,869 | 66 | #include "hts_writer/StreamHtsFileWriter.h"
#include <spdlog/spdlog.h>
#include <memory>
#include <stdexcept>
#include <string>
#include <utility>
namespace dorado {
namespace hts_writer {
StreamHtsFileWriter::StreamHtsFileWriter(const HtsFileWriterConfig& cfg) : HtsFileWriter(cfg) {}
void StreamHtsFileWriter::shu... |
7392d57e7225057ec60239ce6849fa4c898dd0c3c92235cfb16b99c5ec04a705 | C++ | 1,885 | 45 | #include "TestUtils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "splitter/RNAReadSplitter.h"
#include <catch2/catch_test_macros.hpp>
#include <torch/serialize.h>
#include <filesystem>
#include <vector>
#define TEST_GROUP "[RNASplitTest]"
CATCH_T... |
8916d4424027e54360fea4fdedab63d47ecee77d5db82ad56a0c49e646b0913d | C++ | 1,885 | 57 | #include "ChunkBenchmarks.h"
namespace dorado::basecall {
ChunkBenchmarks::ChunkBenchmarks() {}
std::optional<const ChunkBenchmarks::ChunkTimings> ChunkBenchmarks::get_chunk_timings_internal(
const GPUName& gpu_name,
const ModelName& model_name) const {
// Try looking up the specified gpu name di... |
4a885120c439374bb364f49f3dd530685033b1a3f740810205a581d5f521cab9 | C++ | 1,888 | 43 | #include "modbase/MotifMatcher.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#define TEST_GROUP "[modbase_motif_matcher]"
using std::make_tuple;
namespace {
// clang-format off
const std::string SEQ = "AACCGGTTACGTGGACTGACACTAAA";
// " CG CG ... |
4cb6140638c3bc686f097a0c80e5244f9cdffd4068b73bcbdd5cdadd5da71b07 | C++ | 1,889 | 62 | #include "faidx_utils.h"
#include <htslib/faidx.h>
#include <algorithm>
#include <iostream>
#include <memory>
#include <stdexcept>
namespace kadayashi::hts_utils {
namespace {
struct CharDestructor {
void operator()(char* ptr) { hts_free(ptr); };
};
using CharPtr = std::unique_ptr<char, CharDestructor>;
} //... |
c9dd8513a080f6a4537b1519a1c045d675e1801d112aeeffe4a87f5099ebcaa5 | C++ | 1,899 | 62 | #include "demux/BarcodeClassifierSelector.h"
#include "demux/barcoding_info.h"
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[dorado::demux::BarcodeClassifierSelector]"
namespace {
CATCH_TEST_CASE(TEST_GROUP " constructor does not throw", TEST_GROUP) {
CATCH_REQUIRE_NOTHROW(dorado::demux::Barcode... |
b91fa1595099d417d742feed687ee2778d0c8338a0aee44300e2794a183cd677 | C++ | 1,979 | 42 | #include "correct/types.h"
#include "torch_utils/tensor_utils.h"
#include <ostream>
#include <tuple>
namespace dorado::correction {
std::ostream& operator<<(std::ostream& os, const OverlapWindow& ovl) {
os << "overlap_idx = " << ovl.overlap_idx << ", win_tstart = " << ovl.win_tstart
<< ", win_tend = " <<... |
c7a122e8327e3b5532890aa7c325c67cb2b22e1d110ca38bed2b52a9d9c03936 | C++ | 2,007 | 53 | #include "model_gru.h"
namespace dorado::secondary {
ModelGRU::ModelGRU(const MustConstructWithFactory& ctor_tag,
const int32_t num_features,
const int32_t num_classes,
const int32_t gru_size,
const int32_t num_layers,
cons... |
c6ae003d6aaa844206fbb8d354dfc8fed672051fd00b30a4f84702b970febcd6 | C++ | 2,052 | 84 | #include "string_utils.h"
#include <cstring>
#include <sstream>
#include <vector>
namespace kadayashi {
bool stoi_catch(int &dest, const char *s) {
try {
size_t tmp = 0;
dest = std::stoi(s, &tmp);
if (tmp == 0 || tmp != strlen(s)) {
return false;
}
} catch (...) {
... |
ee34fd9e452e64146001a6a9e8f7ba3578ddaac70fc82d97e7cabb2e6d514d06 | C++ | 2,079 | 66 | #include "hts_utils/header_sq_record.h"
#include "utils/sequence_utils.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <array>
#include <cstdint>
#include <numeric>
namespace {
constexpr std::array to_upper = []() {
std::array<unsigned char, 256> lookup;
std::iota(std::begin(lookup), std::end... |
4c438bceb4ea1ee3c493fbdcd0610813d0157fe8be82ee43bab0d6e2d1f47bef | C++ | 2,083 | 72 | #include "channelstatelayout.h"
QString ChannelStateLayout::getLabelStyle(bool state)
{
const QString styledEnable = "QLabel {\
font-family: HarmonyOS Sans SC;\
font:bold 18px;\
color: black;\
background-color:#B6EFAF;\
border: 1px solid #88A6C9;... |
cfdc726270312bfe8876030d65da79f73b1c2bde064c7ae1f12f9bda434816e3 | C++ | 2,102 | 43 | #include "utils/parameters.h"
#include <algorithm>
#include <thread>
namespace dorado::utils {
ThreadAllocations default_thread_allocations(int num_devices,
int num_modbase_threads,
bool enable_aligner,
... |
30ec413dd093117323790b6e854328aaeacdd488752c48c669e5d92b15208935 | C++ | 2,127 | 64 | #include "demux/adapter_info.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <map>
namespace {
// This map should contain any primer sets defined in adapter_primer_kits.cpp
// that must be specified in the AdapterInfo object in order to be searched for.
// If one of these entries is specifie... |
6b22bd06e29f3db1fa7e46c347ae6c8235c1e0ae928bb51532c2ced89b7b08bc | C++ | 2,147 | 57 | #include "basecall/ModelRunner.h"
#include "basecall/crf_utils.h"
#include "decode/Decoder.h"
#include "model/CRFModel.h"
namespace dorado::basecall {
ModelRunner::ModelRunner(const config::BasecallModelConfig &model_config)
: m_config(model_config),
m_decoder(decode::create_decoder(c10::DeviceType... |
80b0f7957360b4170d1e34d0872c959042ede922e60f1a27ef9f4db8cc8a64ba | C++ | 2,153 | 60 | #include "nn/TxModules.h"
#include <ATen/ops/scaled_dot_product_attention.h>
#include <c10/core/DeviceType.h>
#include <c10/core/TensorOptions.h>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators_range.hpp>
#include <spdlog/spdlog.h>
#include <torch/nn.h>
#include <torch/version.h>
... |
b7f466d07b2ff6df93d5a90e6950b38b4035e853cb51110a3d2392ffd906c41a | C++ | 2,172 | 102 | #include "global_variable.h"
C_general_stat::C_general_stat()
{
read_max_length = 0;
read_length = 0;
reads_number = 0;
base_number = 0;
a_number = 0;
c_number = 0;
g_number = 0;
t_number = 0;
n_number = 0;
// a_ratio,c_ratio,g_ratio,t_ratio,n_ratio=0;
q20_num = 0;
q30_num = 0;
}
C_reads_pos_base_stat::C_r... |
2b8f63fb9a3d5cc39e41a3e032ae777bd2560d881ac0cc684b155c90d12aa98f | C++ | 2,182 | 99 | #include "configparam.h"
#include "configparammanager.h"
#include <QDebug>
ConfigParamManager::ConfigParamManager()
{
}
QStringList ConfigParamManager::getFrequencyItemList()
{
static QStringList items;
if(0x00 == items.size()){
for(int i=20;i<=1000;i+=10){
items.append(QS... |
a6aa4f6321714503ce286022d5a100c7e7516256789d82f2eeea8447af278902 | C++ | 2,183 | 68 | #include <iostream>
#include <string>
#include <fstream>
#include "process_argv.h"
#include "global_parameter.h"
#include "peprocess.h"
#include "seprocess.h"
#include <exception>
#ifdef _PROCESSHTS
#include "processHts.h"
#endif
#include "processStLFR.h"
//#include "mGzip.h"
//vector<threadDataInfo> C_global_paramet... |
04df93bdcdf74c619de402b6d6a34baeb424a3a5ae2a285e2ac8a17e5f60c141 | C++ | 2,315 | 79 | #include "modbase/MotifMatcher.h"
#include "config/ModBaseModelConfig.h"
#include <nvtx3/nvtx3.hpp>
#include <iterator>
#if defined(__GNUC__) && !defined(__clang__) && !defined(__INTEL_COMPILER)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
#endif
#include <regex>
#if defined(__G... |
3ad583b6bb16c6a5a1f0b07bf17a8d8683f14fd09a1fff7eeae577bd5ec3bf38 | C++ | 2,321 | 93 | #include "serial.h"
#include <QDebug>
#include "event.h"
Serial::Serial()
{
}
void Serial::run()
{
//CH343 ²âÊÔ
//Physical Acoustics
//Multiplexer
//6790
//21970
serial = new QSerialPort;
//»ñÈ¡¿ÉÓô®¿ÚÃûµ½ÏÂÀÀ¸
QList<QSerialPortInfo> list = QSerialPortInfo:... |
ec3800d6199ade0b00b2dee4907c75f8f06632a2743833fb2b4987d439373c76 | C++ | 2,385 | 82 | #include "hts_utils/fai_utils.h"
#include <htslib/faidx.h>
#include <spdlog/spdlog.h>
#include <fstream>
#include <sstream>
#include <stdexcept>
#include <string>
namespace dorado::utils {
std::filesystem::path get_fai_path(const std::filesystem::path& in_fastx_fn) {
char* idx_name = fai_path(in_fastx_fn.string... |
d3e5c8e1159b41786d55e04b8d96b38e126a6e02a5dfbd81a1e3d4c301ed8f7b | C++ | 2,432 | 74 | #include "csv_helpers.h"
#include "utils/SeparatedStream.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
namespace dorado::batchsize_benchmarks {
namespace detail {
std::optional<ParsedLine> csv_try_parse_line(std::string_view line) {
// Ignore empty lines.
if (line.empty()) {
return ... |
39e0f302b3c39ee088a4bc4d133a94d746e6f4f39f886d5072492cb61bd3c026 | C++ | 2,542 | 77 | #include "read_pipeline/nodes/WriterNode.h"
#include "hts_writer/HtsFileWriter.h"
#include "hts_writer/SummaryFileWriter.h"
#include "hts_writer/interface.h"
#include "read_pipeline/base/messages.h"
#include "utils/stats.h"
#include <utility>
namespace dorado {
WriterNode::WriterNode(std::vector<std::unique_ptr<hts... |
32cf1d35a61cb4b1f5c874a43d6f34cf500320d3b004435c71cf5fe2b67acd60 | C++ | 2,562 | 83 | #include "secondary/architectures/model_torch_base.h"
namespace dorado::secondary {
torch::Device ModelTorchBase::get_device() const {
// Get the device of the first parameter as a representative.
for (const auto& param : this->parameters()) {
if (param.defined()) {
return param.device();
... |
11663057085ac01382ff76a43f9a77bf0049ce723bdce93ef983fd4c1a74811c | C++ | 2,603 | 92 | #include "medaka_bamiter.h"
#include "hts_utils/bam_utils.h"
#include "utils/cigar.h"
#include <htslib/sam.h>
#include <algorithm>
#include <cerrno>
#include <cstring>
namespace dorado::secondary {
int32_t mpileup_read_bam(void *data, bam1_t *b) {
HtslibMpileupData *aux = reinterpret_cast<HtslibMpileupData *>(... |
01a711350bea009e9c0b5d0a3578327c10ac65fa773c1cec1e1cafafd8b19482 | C++ | 2,616 | 73 | #include "torch_utils/torch_utils.h"
#include "compat/compat_utils.h"
#include <c10/util/Backtrace.h>
#include <torch/torch.h>
#include <torch/version.h>
#if DORADO_CUDA_BUILD
#include <c10/cuda/CUDAAllocatorConfig.h>
#endif // DORADO_CUDA_BUILD
namespace dorado::utils {
void initialise_torch() {
// By defaul... |
cd4668dfc020880e2fe8d1c4f919d19eae637cad3bc144a3e44a6c569a2fad93 | C++ | 2,623 | 73 | #include "read_pipeline/nodes/ReadFilterNode.h"
#include "read_pipeline/base/messages/ReadCommon.h"
#include <spdlog/spdlog.h>
namespace dorado {
void ReadFilterNode::input_thread_fn() {
at::InferenceMode inference_mode_guard;
Message message;
while (get_input_message(message)) {
// If this mes... |
bdd535d042a6eab6715f3fcef1936259a70406d1c90b0c076ca8fe5d3e2c981f | C++ | 2,626 | 77 |
#include "secondary/consensus/sample_collate_utils.h"
#include <spdlog/spdlog.h>
#include <stdexcept>
namespace dorado::secondary {
std::vector<int64_t> compute_collated_padded_shape(const std::vector<Sample>& buffered_samples) {
if (std::empty(buffered_samples)) {
return {};
}
// The +1 is fo... |
e36121438913b6a5b01c48f97a6e363679adfe60a5874f4c7d5b7b3ebba33ccf | C++ | 2,712 | 84 | #include "correct/infer.h"
#include "correct/types.h"
#include "utils/memory_utils.h"
#include "utils/string_utils.h"
#include <c10/core/Device.h>
#include <spdlog/spdlog.h>
#include <toml.hpp>
#if DORADO_METAL_BUILD
#include "torch_utils/metal_utils.h"
#endif
#if DORADO_CUDA_BUILD
#include "torch_utils/cuda_utils.h... |
b5912821c77a92797d6354e281d4bffbee8a784f95f1c61b1d7dc2eb38402804 | C++ | 2,774 | 87 | #include "blocked_bloom_filter.h"
#include <spdlog/spdlog.h>
#include <cstdio>
#include <cstring>
#include <memory>
namespace kadayashi {
uint64_t BlockedBloomFilter::m_bbf_hash64(uint32_t i) const { return std::hash<uint64_t>{}(i); }
BlockedBloomFilter::BlockedBloomFilter(int n_hashes, int n_blocks_bits)
... |
463b286732c2111682adb5a8a96d8bab0108d1749ce2a166b749a9ac167222a4 | C++ | 2,804 | 84 | #include <matrix.h>
#include <mex.h>
#include <algorithm>
#include "runningPrctile.cpp"
/* Definitions to keep compatibility with earlier versions of ML */
#ifndef MWSIZE_MAX
typedef int mwSize;
typedef int mwIndex;
typedef int mwSignedIndex;
#if (defined(_LP64) || defined(_WIN64)) && !defined(MX_COMPAT_32)
/* Curren... |
a6e91556a75c57b4bb2405b7267207b7e5ed37959deb0566efda262f49782904 | C++ | 2,813 | 110 | #include "utils/log_utils.h"
#include "utils/tty_utils.h"
#include <spdlog/sinks/stdout_color_sinks.h>
#include <spdlog/spdlog.h>
#ifndef _WIN32
#include <fcntl.h>
#include <unistd.h>
#endif
#include <array>
#include <string>
namespace dorado::utils {
namespace {
/**
* @brief Get the file path associated with a... |
5ee365f5f132b526a0bac87fd7188a9b4ef7f379dd852dc1abfb8c95e25b38d5 | C++ | 2,816 | 77 | #include "config/ModBaseBatchParams.h"
#include "config/ModBaseModelConfig.h"
#include "utils/dev_utils.h"
#include <spdlog/spdlog.h>
#include <toml.hpp>
#include <exception>
#include <filesystem>
#include <stdexcept>
#include <string>
namespace dorado::config {
namespace {
namespace DefaultModBaseParameters {
co... |
72dcc0f7f0ae069bfccf710ffae301b74df955f9bb903d6939d9657575a67bc9 | C++ | 2,816 | 86 | #include "utils/concurrency/async_task_executor.h"
#include <stdexcept>
namespace dorado::utils::concurrency {
AsyncTaskExecutor::AsyncTaskExecutor(MultiQueueThreadPool& thread_pool,
TaskPriority priority,
std::size_t max_queue_size)
:... |
fb27c70b82d6d22d9af33571cd085c96a63fecb3bb0961f03ebb85c8fb0607b4 | C++ | 2,822 | 97 | #include "utils/ResourceLimiter.h"
#include <cassert>
namespace dorado::utils {
ResourceLimiter::ResourceLimiter(std::size_t max_size) : m_max_size(max_size) {
assert(m_max_size > 0);
}
void ResourceLimiter::acquire(WaiterState &waiter, int64_t size) {
// The current approach cannot support a second acquire... |
80531a1aed9dfdef1ad50f917cebd33dfbad140d743dff0427041455e3f4943d | C++ | 2,844 | 84 | #include "torch_utils/cuda_utils.h"
#include <ATen/Context.h>
#include <ATen/ops/allclose.h>
#include <ATen/ops/empty.h>
#include <ATen/ops/rand.h>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
#include <spdlog/spdlog.h>
#de... |
0cead7752cd81d9d074c8336f08cca9a17fa26b5c1fff85160c1316bfdc96e41 | C++ | 2,877 | 86 | #include "utils/paf_utils.h"
#include "utils/alignment_utils.h"
#include "utils/overlap.h"
#include <spdlog/spdlog.h>
#include <iostream>
#include <ostream>
#include <sstream>
namespace dorado::utils {
PafEntry parse_paf(std::istringstream& ss) {
PafEntry entry;
// Read the fields from the stringstream
... |
bfb195b11a7279c9be9e0c44255a51296bb846c432daf935e80a28801d1e98d6 | C++ | 2,894 | 77 | #include "read_pipeline/base/MessageSink.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages/ReadCommon.h"
#include "utils/thread_utils.h"
#include <cassert>
namespace dorado {
MessageSink::MessageSink(size_t max_messages, int num_input_threads)
: m_work_queue(max_messages), ... |
5b4e928ece39f04d4c22dd8310c1a7f8c6878a7663e86bb46fec6fae9ed4f75d | C++ | 2,910 | 108 | #include "utils/time_utils.h"
#include <chrono>
#include <ctime>
#include <sstream>
// Some stdlibs don't support parse()/from_stream() yet, or they can't format a sys_time<> correctly.
#if defined(__cpp_lib_format) && (defined(_GLIBCXX_RELEASE) && _GLIBCXX_RELEASE >= 14)
#define FULL_CHRONO_SUPPORT 1
#else
#define F... |
5dac51ecfd39bc1f6ed94fa1e6f493db1a2903061c41919eb2cb04ef0e090928 | C++ | 2,915 | 86 | #include "utils/concurrency/detail/priority_task_queue.h"
#include <cassert>
#include <iterator>
namespace dorado::utils::concurrency::detail {
void PriorityTaskQueue::queue_producer_task(TaskQueue* producer_queue) {
m_producer_queue_list.push_back(producer_queue);
auto task_itr = std::prev(m_producer_queue_... |
fbdb6acf8fe34585835f91ff856a11e1eab2f770ad52f81f0c41c47e592d645c | C++ | 2,975 | 85 | #include "poly_tail/poly_tail_calculator_selector.h"
#include "poly_tail/poly_tail_calculator.h"
#include "poly_tail/poly_tail_config.h"
#include "utils/types.h"
#include <cassert>
#include <fstream>
#include <sstream>
namespace dorado::poly_tail {
PolyTailCalculatorSelector::PolyTailCalculatorSelector(
con... |
d51f91f1c5fb9fab53954ac1217667908b7fa2192f6e89b103bf980038de5baf | C++ | 2,991 | 96 | #include "TestUtils.h"
#include <spdlog/spdlog.h>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#ifndef _WIN32
#include <unistd.h>
#endif
namespace dorado::tests {
std::filesystem::path get_data_dir(const std::string& sub_dir) {
const std::filesystem::path root_path("./tests/data... |
c41a78abfe8fc30c252cf538b6baa1be5d53a550c5d710dc7319486f2b1173a2 | C++ | 3,004 | 76 | #include "batchsize_helpers.h"
#include "SpeedEntry.h"
#include "compiled_timings.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <ranges>
#include <stdexcept>
namespace dorado::batchsize_benchmarks {
namespace {
// Fallback for platforms that don't support std::ranges::to() yet.
#if !defined(_LIBCPP_... |
1ee2dbb3c9029a0585f0aa5ef73dac2bc601a1674c148e0b5fde6c9e527fa29e | C++ | 3,073 | 126 | #include "event.h"
#include "QDebug"
Event::Event()
{
this->stream = NULL;
this->stream_length = 0x00;
this->head = 0x00;
this->event_type = EVENT_RESERVE;
this->data_length = 0x00;
this->crc = 0x00;
this->data = NULL;
}
Event::Event(unsigned char *stream,unsigned int size)
{
... |
3cb93678e4941f9d1ee00c402e531ddf63ad6b9b504417a725d11c4d9a2e1b5b | C++ | 3,090 | 79 | #include "hts_writer/SummaryFileWriter.h"
#include "hts_utils/hts_types.h"
#include "utils/string_utils.h"
#include <catch2/catch_message.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <htslib/sam.h>
#include <sstream>
#include <string_view>
#define TEST_GROU... |
1ef55f5337ddfe24e8a0950f8360de1ce5dd167c6c35fd87036d87a172ebadf6 | C++ | 3,162 | 91 | #include "summary_info.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 <spdlog/spdlog.h>
namespace dorado::cli {
namespace {
void update_alignment_counts(HtsReader& file, AlignmentCounts& alignment_counts) {
... |
9513039f4d88643287e7c6b0b158b2a147b81db2a8429879ed2e28c4d09b9cdf | C++ | 3,167 | 98 | #include "TestUtils.h"
#include "utils/overlap.h"
#include "utils/paf_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <filesystem>
#include <fstream>
#include <sstream>
#include <string>
#include <string_view>
#include <vector>
#define TEST_GROUP "[paf_utils]"
CATCH_TEST_CASE("PafUtilsTest: Test round tri... |
57a3b7f4fee181f19ec05fcfb33b25bf88ac7496d8dc4b985e7ff7cdaa70ccbb | C++ | 3,199 | 82 | #include "resume_loader/ResumeLoader.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/HtsReader.h"
#include "utils/tty_utils.h"
#include <htslib/sam.h>
#include <indicators/indeterminate_progress_bar.hpp>
#include <spdlog/spdlog.h>
#include <filesystem>
#include <memory>
namespace d... |
e64d737e20277574999a65d7ab204b110b4c1d71689a2eb40f71ba54cf1abcb2 | C++ | 3,272 | 90 | #include "utils/rle.h"
#include <catch2/catch_test_macros.hpp>
#include <cstdint>
#include <string>
#include <tuple>
#include <vector>
#define TEST_GROUP "[RLE]"
#if defined(__clang__) && defined(__GLIBCXX__)
// See https://github.com/catchorg/Catch2/issues/2923
template <>
struct std::tuple_size<Catch::Decomposer>... |
1188b8b2803772341f344b53c8f34e8fbc6d85afce2a0c56cb40114d1114156f | C++ | 3,281 | 93 | #include "CorrectionPafReader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h"
#include "utils/paf_utils.h"
#include "utils/timer_high_res.h"
#include <spdlog/spdlog.h>
#include <fstream>
#include <vector>
namespace dorado {
void CorrectionPafReader::pro... |
1d7355329d3a865457aadbc4a927e077fda5b9ddf7fdf9dfca8cbaefb1199ba4 | C++ | 3,285 | 101 | #include "hts_writer/StructuredHtsFileWriter.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "hts_writer/HtsFileWriter.h"
#include "hts_writer/Structure.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <memory>
#include <stdexcept>
#include <st... |
1b92c88446c89019b0ecee88bb7f1bbb79f630cd89361f9df23635b3ce24ce4e | C++ | 3,341 | 119 | #include "model_resolver/ModelSources.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <ios>
#include <sstream>
namespace dorado::model_resolution {
namespace fs = std::filesystem;
bool check_model_path(const fs::path& model_path) {
try {
const auto& p = fs::weakly_canonical(model_path);
... |
e3cacf0298de5cf62bdde0b663ddfd30b3ac03cf7ef379642a5a8eb4dff7cb7f | C++ | 3,377 | 87 | #include "read_pipeline/nodes/DuplexReadTaggingNode.h"
#include "MessageSinkUtils.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[read_pipeline][DuplexReadTaggingNode]"
CATCH_TEST_CASE("DuplexReadTaggingNode", TEST_GROUP) {
dorado::PipelineDes... |
aba42fc0190588f81677bf9a7acda0dc05ed8746b401bd4736fad008ea4f0d5f | C++ | 3,379 | 96 | #include "splitter/myers.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#define CUT_TAG "[myers]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
using dorado::splitter::EdistResult;
using dorado::splitter::myers_align;
DEFINE_TEST("Basic alignment,... |
e650a2b2da677e54590d4e636aae631d093b964a1ae6cdbd9be02bd2632125ed | C++ | 3,398 | 97 | #include "config/common.h"
#include <toml.hpp>
#include <stdexcept>
#include <unordered_map>
namespace keys {
namespace {
const std::string ACTIVATION{"activation"};
}
} // namespace keys
namespace dorado::config {
static const std::unordered_map<std::string, SublayerType> sublayer_map = {
{"clamp", Subla... |
6cf78e5192d72d0ba77371a620dd0ef6154bd473100d8e436b3eeda111e57896 | C++ | 3,437 | 115 | #include "hts_utils/header_utils.h"
#include "utils/string_utils.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <ostream>
#include <sstream>
#include <string_view>
#include <unordered_map>
#include <vector>
namespace {
using namespace dorado::utils;
static std::unordered_map<std::string, HeaderLineT... |
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