sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
49fdfb033ed2a9a0983a3213b6ee0d881fac54c6f16d26e5eb69c5aae50ddace | C++ | 6,991 | 140 | #include "SpeedEntry.h"
#include "batchsize_helpers.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers.hpp>
#include <limits>
#include <stdexcept>
#define CUT_TAG "[batchsize_benchmarks]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
using namespace dorado::ba... |
e3e722b348ce239bf95503aff9d7c67234ed4a6486c34eb84682e5dfe90026ad | C++ | 7,007 | 175 | #include "hts_writer/HtsFileWriterBuilder.h"
#include "hts_utils/hts_file.h"
#include "hts_writer/HtsFileWriter.h"
#include "hts_writer/StreamHtsFileWriter.h"
#include "hts_writer/Structure.h"
#include "hts_writer/StructuredHtsFileWriter.h"
#include "utils/tty_utils.h"
#include <spdlog/spdlog.h>
#include <cstdio>
#i... |
ae7f6221be90de18029cd0d92b220356a8caae2b6044207e6594f648bda6414e | C++ | 7,119 | 214 | #include "read_pipeline/base/HtsReader.h"
#include "hts_utils/HeaderMapper.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#includ... |
9bf6735db6118132ee8f4073023294727cf992d0630ed4cc2289dbd856d4ccc7 | C++ | 7,153 | 255 | #include "alignment/bed_file.h"
#include "utils/PostCondition.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <fstream>
#include <iomanip>
#include <optional>
#include <sstream>
#include <string_view>
#include <tuple>
namespace dorado::alignment {
namespace {
constexpr std::size_t MIN_COLS{3}... |
f8adaddb19d12e21b96d8800d624a7c91e76172a91f286d4477105a2063131fa | C++ | 7,178 | 180 | #include "secondary/architectures/model_herro.h"
#include "secondary/architectures/model_weights.h"
#include <ATen/TensorIndexing.h>
#include <algorithm>
namespace dorado::secondary {
namespace {
constexpr int64_t BASE_ALPHABET_SIZE = 12;
constexpr int64_t BASE_EMBEDDING_SIZE = 6;
constexpr int64_t INPUT_CHANNELS ... |
a7a34131bf469cd8ffe2d65865b5bf09bf9f771bc7c14cbaeccde8492ae7a8d7 | C++ | 7,243 | 208 | #include "secondary/common/region.h"
#include "secondary/common/window.h"
#include "secondary/consensus/window_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/matchers/catch_matchers_string.hpp>
#include <cstdint>
#include <string>
#include <unordere... |
d4a814617ca2d3da9612021b7152b5eaa225c9a30ed041b03f82be3c0add979d | C++ | 7,418 | 198 | #include "secondary/consensus/consensus_utils.h"
#include <cassert>
#include <cstddef>
#include <ostream>
#include <sstream>
#include <stdexcept>
namespace dorado::secondary {
/**
* \brief Copy the draft sequence for a given sample, and expand it with '*' in places of gaps.
*/
std::string extract_draft_with_gaps(c... |
0c4cea69e7a14b6733829bc3e89bf47f23be741fc4ebf1eb4d9839d48a08e30c | C++ | 7,429 | 160 | #include "read_pipeline/nodes/ReadFilterNode.h"
#include "MessageSinkUtils.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <ATen/ops/empty.h>
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[read_pipeline][ReadFilterNode]"
namespace {
auto make_filtered_pipeline(std::vector<dorado::Mess... |
e74510e022c3da007bb126541804bc00a05d0f945526bd03a84f968b028568e9 | C++ | 7,473 | 169 | #include "read_pipeline/base/stitch.h"
#include "read_pipeline/base/messages/ReadCommon.h"
#include "utils/math_utils.h"
#include <ATen/ops/zeros.h>
#include <catch2/catch_test_macros.hpp>
#include <cstdint>
#include <memory>
#include <string>
#include <vector>
#define TEST_GROUP "[utils]"
// clang-format off
cons... |
bb9672d9cacdd82ec49b267a5e0d3b0546a55b32a7517e3bc23d9e0029993caa | C++ | 7,493 | 185 | #include "utils/sequence_utils.h"
#include <ATen/TensorIndexing.h>
#include <catch2/catch_test_macros.hpp>
using Slice = at::indexing::Slice;
using namespace dorado;
#define TEST_GROUP "[utils][realign_moves]"
CATCH_TEST_CASE("Realign Moves No Error", TEST_GROUP) {
std::string query_sequence = "ACGTACGTACGTACGT... |
e4186e673ebfa39acca73698879bea6e5a5cb38faa7a31297e5cce0b65a2ba58 | C++ | 7,513 | 253 | #include "controldialog.h"
#include "hardwarethread.h"
#include "loaddata.h"
#include "main_widget.h"
#include "ui_mainwidget.h"
#include <QDebug>
#include <QString>
#include <QMessageBox>
#include <buttonstyle.h>
#include <scrollareastyle.h>
#include <channelselectlayout.h>
#include <QFileDialog>
#incl... |
dc15918013b51a86c19f7e8cd335c407aef8f76bcbc1e8f3f0d1d010e25a9052 | C++ | 7,561 | 181 | #include "utils/concurrency/detail/priority_task_queue.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#define CUT_TAG "[dorado::utils::concurrency::detail::PriorityTaskQueue]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
#define DEFINE_CATCH_SCENAR... |
b7cc397957eae2215982ed8b31f3eacf25908bcc0fb28cc709b991196d323a95 | C++ | 7,624 | 186 | #include "TestUtils.h"
#include "config/ModBaseModelConfig.h"
#include "config/common.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <string>
#define TEST_GROUP "[modbase_config]"
namespace fs = std::filesystem;
using namespace dorado::config;
namespace {
voi... |
b53a8d4302335268e1fa5f7d1a535ffe25bd8a97bae0ff565f6a5ee689d44721 | C++ | 7,825 | 227 | #include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "data_loader/DataLoader.h"
#include "dorado_version.h"
#include "model_downloader/model_downloader.h"
#include "model_resolver/ModelResolver.h"
#include "model_resolver/Models.h"
#include "models/model_complex.h"
#include "models/models.h"
#include "utils/l... |
fe1f277e5cab30f2fd0433ada270c9480708e82c1b166a7b351aeca5ed18f256 | C++ | 7,830 | 209 | #include "utils/concurrency/async_task_executor.h"
#include "utils/PostCondition.h"
#include "utils/concurrency/synchronisation.h"
#include <catch2/catch_test_macros.hpp>
#include <atomic>
#include <memory>
#include <thread>
#include <utility>
#define CUT_TAG "[dorado::utils::concurrency::AsyncTaskExecutor]"
#defin... |
7aaacedeb85b9d79cf04d181f9c272a214eeae339af9c21735ce84eba5205d1b | C++ | 7,895 | 184 | #include "torch_utils/trim.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <sstream>
namespace dorado::utils {
namespace detail {
// Out of line to avoid pulling exception handling and string formatting into the header.
[[noreturn]] void trim_throw(std::size_t size, const std::p... |
df4a068a50857e67bb6165bfcf514213517fb70931a2e85fc8104cdd40523597 | C++ | 7,928 | 198 | #include "read_pipeline/nodes/AdapterDetectorNode.h"
#include "demux/AdapterDetector.h"
#include "demux/Trimmer.h"
#include "demux/adapter_info.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/PostCondition.h"
#include "... |
18d47da29ac2f1daa07650454d0c6351de9f1cb89d20f01037d4724d1a93db75 | C++ | 7,931 | 221 | #include "plotdialog.h"
//#include <QRandomGenerator>
#include <QtCharts/QChartView>
#include <QVBoxLayout>
#include <QHBoxLayout>
#include <QFrame>
#include <QLabel>
#include <QPushButton>
#include <QPainter>
#include <QColor>
#include <QPen>
#include <QtGlobal>
// ¹¹Ô캯ÊýÀàÃû¸ÄΪ PlotDialog
PlotDialog... |
80be5d1827b9288240f415b6df80f290523ba26bd99a22f0b35dbaa13fc1c383 | C++ | 7,975 | 217 | #include "secondary/common/vcf_writer.h"
#include "dorado_version.h"
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <algorithm>
#include <cstdint>
#include <cstring>
#include <sstream>
#include <stdexcept>
#include <string_view>
namespace dorado::secondary {
namespace {
void ensure_buffer_initialized(ks... |
48810a834db9b6c94f407207261ff2708ce32300cb64b7a34493455e4851c8ba | C++ | 8,090 | 198 | #include "torch_utils/tensor_utils.h"
#include <catch2/benchmark/catch_benchmark.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <spdlog/spdlog.h>
#include <torch/torch.h>
#include <cstdlib>
#include <random>
#define CUT_TAG "[TensorUtils]"
CATCH_TEST_CASE(CUT... |
d20b0aae220e935b669c8c2c62353873b1f86b1263d1f89e191c9159a1919d08 | C++ | 8,219 | 227 | #include "secondary/features/kadayashi_utils.h"
#include <spdlog/spdlog.h>
#include <cassert>
#include <cstdio>
#include <fstream>
#include <memory>
#include <stdexcept>
#include <string_view>
namespace dorado::secondary {
namespace {
template <typename T>
void read_checked(std::ifstream& ifs,
T*... |
a8868f710a2be3ff6bff2629e19a99df37398c755479dc88c8cd26fc90b00010 | C++ | 8,281 | 214 | #include "api/runner_creation.h"
#include "basecall/ModelRunner.h"
#include "basecall/crf_utils.h"
#include "config/ModBaseModelConfig.h"
#include "nn/KoiUtils.h"
#if DORADO_METAL_BUILD
#include "basecall/MetalModelRunner.h"
#elif DORADO_CUDA_BUILD
#include "basecall/CudaCaller.h"
#include "basecall/CudaModelRunner.h... |
5c71c1adc8c55ac8291462044886299ab433522de75d498d88256c875fee35b8 | C++ | 8,434 | 173 |
#include "secondary/architectures/model_factory.h"
#include "model_gru.h"
#include "model_latent_space_lstm.h"
#include "model_slot_attention_consensus.h"
#include "model_variant_perceiver.h"
#include "secondary/architectures/model_config_validation.h"
#include "secondary/architectures/model_weights.h"
#include "seco... |
5e96a169e429eb4d5a4062b15a442c3f703adee7978404b3ad3aa9191b09e8a9 | C++ | 8,446 | 248 | #include "utils/concurrency/synchronisation.h"
#include "utils/PostCondition.h"
// libtorch defines a CHECK macro, but we want catch2's version for testing
#include <catch2/catch_test_macros.hpp>
#include <atomic>
#include <chrono>
#include <thread>
using namespace std::chrono_literals;
using test_clock = std::chro... |
9238fdd7fa8bf1bb7bc76f44d9ef2ce89345b8f91772970f3537210a03b8d2ad | C++ | 8,574 | 245 | #include "loaddata.h"
#include <QApplication>
#include <QFile>
#include <QTextStream>
#include <QStringList>
#include <QDebug>
#include <vector>
LoadData::LoadData()
{
}
//// ¶þάÊý×éÀàÐͶ¨Òå
//typedef double InputData[ROWS][COLS];
/**
* @brief ¼ÓÔØCSVÎļþÊý¾Ýµ½¶þάÊý×é
* @param filePath CSVÎļþ... |
e913013043ad0e2d352551b21adc74a7dcca7417e4b89a791978ce36a985e297 | C++ | 8,651 | 197 | #include "CUDADecoder.h"
#include "torch_utils/cuda_utils.h"
#include "torch_utils/gpu_profiling.h"
#include <ATen/TensorIndexing.h>
#include <ATen/ops/arange.h>
#include <ATen/ops/empty.h>
#include <c10/cuda/CUDAGuard.h>
#include <nvtx3/nvtx3.hpp>
#include <numeric>
extern "C" {
#include "koi.h"
}
namespace dorad... |
ef6091ec1ec4997e0f4d00e47fe1d511ceb7c2c76bf97ee6406348b90e0309d2 | C++ | 8,713 | 234 | #include "basecall/MetalCaller.h"
#include "MPSCaller.h"
#include "MetalCallerTask.h"
#include "MetalLSTMCaller.h"
#include "torch_utils/metal_utils.h"
#include "utils/thread_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <chrono>
#include <cstdint>
#include <cstdlib>
#include <memory>
#include <m... |
e6b07d67bfab89ac98f452e3b2a90f67cee03100570b963a3e5a257fa66d8321 | C++ | 8,799 | 232 | //
// Created by berry on 2020-08-11.
//
#ifdef _USEMGZIP
#include "mGzip.h"
using namespace::std;
bool mGzip::check_mGzip(string filePath) {
bool whether_mGzip=false;
// gzFile in=gzopen(filePath.c_str(),"rb");
FILE* in=fopen(filePath.c_str(),"rb");
if(in==NULL){
cerr<<"Error:fail to open file:"... |
b94462937d2287996645fa551c354c50c80160e221ffe186b3dc6cce4592a127 | C++ | 8,945 | 295 | #include "downloader.h"
#include "models/models.h"
#include "utils/crypto_utils.h"
#include <elzip/elzip.hpp>
#include <spdlog/spdlog.h>
#include <url.hpp>
#include <filesystem>
#include <sstream>
#if DORADO_MODELS_HAS_HTTPLIB
#ifndef _WIN32
// Required for MSG_NOSIGNAL and SO_NOSIGPIPE
#include <sys/socket.h>
#inc... |
757209cf3820a6d5b1d80f0618a011c9622624cd44625fe8a20ca890e2c40c25 | C++ | 8,992 | 226 | #include "utils/string_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <iterator>
#include <limits>
#include <sstream>
#include <string>
#include <string_view>
#define CUT_TAG "[dorado::utils::string_utils]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG... |
a96d199eecfd19066aee560cd2134907fd4b5ddc57baae1f9ff5da8d4be16314 | C++ | 9,007 | 208 | /*
* sample_sheet_test.cpp
*
* Created on: August 8, 2022.
* Proprietary and confidential information of Oxford Nanopore Technologies, Limited
* All rights reserved; (c)2022: Oxford Nanopore Technologies, Limited
*/
#include "utils/SampleSheet.h"
#include "TestUtils.h"
#include <catch2/catch_test_macros.hpp... |
3ec06a63d3be61130c5b2afb03e82368bd48b00a26892383039666612cbf7d31 | C++ | 9,072 | 222 | #include "read_pipeline/nodes/BaseSpaceDuplexCallerNode.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "torch_utils/duplex_utils.h"
#include "utils/sequence_utils.h"
#include "utils/thread_utils.h"
#include <cxxpool.h>
#include <edlib.h>
#include <... |
ef6ee2f7017341d38ef8b6b1729c676a63a3f3acbd93120abbccd9884a7cd683 | C++ | 9,082 | 202 | #include "TestUtils.h"
#include "models/kits.h"
#include "models/models.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <set>
#include <stdexcept>
#include <tuple>
#define TEST_TAG "[ModelUtils]"
CATCH_TEST_CASE(TEST_TAG " Get model sample rate by name") {
C... |
111862c03d44c29e8401dc3c4e8eda379952ae23d853a01646df6376cddffd64 | C++ | 9,097 | 300 | #include "event.h"
#include "hardwarethread.h"
#include <QDebug>
#include <QSerialPort>
#include <QSerialPortInfo>
HardwareThread::HardwareThread()
{
this->run_flag = false;
serial = NULL;
}
void HardwareThread::setConfigParam(ConfigParam &p)
{
this->param.row = p.row;
this->param.col... |
a3579f481167f481f434febca3228eddd80a9064b30972eaa98a2922f1ccfde3 | C++ | 9,211 | 239 | #include "read_pipeline/nodes/BarcodeClassifierNode.h"
#include "demux/BarcodeClassifier.h"
#include "demux/Trimmer.h"
#include "demux/barcoding_info.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages.h"
#include "read_pipeline/base/messages/SimplexRead... |
e8f16293a8650894bd497c7a90d96225e9e2e8ddecba3f6676546ab646f7e3b4 | C++ | 9,236 | 255 | #include "bam_tagging.h"
#include "kadayashi_utils.h"
#include "local_haplotagging.h"
#include "pipeline.h"
#include "secondary/common/bam_file.h"
#include <htslib/bgzf.h>
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <cassert>
#include <cstdlib>
#include <sstream>
#ifdef NDEBU... |
81abf19465d838d37c46af0d42d1ffb6033573ae542bcd377927d87301a9e8fe | C++ | 9,241 | 228 | #include "MessageSinkUtils.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "read_pipeline/base/terminate_options.h"
#include "read_pipeline/nodes/NullNode.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#define ... |
db242c715546d59f52030439b2a4edb82e3d2cc26ac29d1480ec9d6aea60d628 | C++ | 9,299 | 234 | #include "alignment/sam_utils.h"
#include "catch2/matchers/catch_matchers.hpp"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
#include <algorithm>
#include <numeric>
#define CUT_TAG "[sam_utils]"
using namespace dorado;
usi... |
76625844683cb1bf09aaad65da83be2fb83b64699844063c89269620e1d32008 | C++ | 9,492 | 247 | #include "read_pipeline/nodes/WriterNode.h"
#include "TestUtils.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "hts_writer/HtsFileWriter.h"
#include "hts_writer/HtsFileWriterBuilder.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pi... |
0758b6f4d57693566ab15cb0332255ff75ea01ac4f529c04329cb1aac13caf0f | C++ | 9,546 | 250 | #include "basecall/crf_utils.h"
#include "config/BasecallModelConfig.h"
#include "model/CRFModel.h"
#include "model/TxModel.h"
#include "torch_utils/tensor_utils.h"
#include "utils/memory_utils.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cstddef>
#include <optional>
#... |
c2d25562ee5e142d3dd4393d2778099c1afa3156cdc7b5c18e2eb5a0b9f0f665 | C++ | 9,577 | 348 | /****************************************************************************
**
** Copyright (c) 2009-2018 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/PointCoordinates.cpp#5 $$Change: 2549 $
** $DateTime: 2018/12/28 22:24:20 $$Author: bbarber $
**
***************************************... |
82d0126664b5b751a1c8e1be96f02b5173ff3e84a8b7c5938d67a74d8f401655 | C++ | 9,634 | 264 | #include "utils/thread_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <array>
#include <atomic>
#include <chrono>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <optional>
#include <sstream>
#include <string>
#include <thread>
#ifdef _WIN32
#include <Windows.h>
#elif defined(__A... |
cd6030e17cd1ad5adb6a562e93dbb60e5e6b845bcc8a56f0d014750b0aed9e98 | C++ | 9,649 | 242 | #include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "poly_tail/poly_tail_calculator_selector.h"
#include "poly_tail/poly_tail_config.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/SimpleExecutor.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "read_pipeline/... |
58b40d7b36dc4cf8a3ec20a95e2a792d32a28706802181f45abe952789f0cf35 | C++ | 9,753 | 272 | #include "utils/context_container.h"
// libtorch defines a CHECK macro, but we want catch2's version for testing
#include <catch2/catch_test_macros.hpp>
#define CUT_TAG "[dorado::ContextContainer]"
namespace {
struct SomeClass {
int value;
};
struct SomeBaseClass {};
struct SomeDerivedClass : public SomeBaseC... |
65206c5b412684a7f449406d7e7b86ccb8280e785bf47dc248bc4fd4be2f8978 | C++ | 9,832 | 277 | #include "modbase/ModBaseCaller.h"
#include "ModBaseScaler.h"
#include "config/ModBaseModelConfig.h"
#include "modbase/MotifMatcher.h"
#include "nn/ModBaseModel.h"
#include "utils/sequence_utils.h"
#include "utils/thread_utils.h"
#include <nvtx3/nvtx3.hpp>
#include <spdlog/spdlog.h>
#include <chrono>
#include <cstdd... |
ece441bfa555ef1a1c8f900bbe55bbcb8cacf35b6b1004e8ea98eb6aae8b5c87 | C++ | 9,845 | 210 | #include "TestUtils.h"
#include "demux/parse_custom_kit.h"
#include "demux/parse_custom_sequences.h"
#include "utils/barcode_kits.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
namespace fs = std::filesystem;
CATCH_TEST_CASE("Parse custom single ended barcode arrangement... |
cdec1da8e775bae4273d5f31826770f6c1dc997ac20a2001884d9f6518abdee2 | C++ | 9,851 | 240 | #include "ProgressTracker.h"
#include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "demux/adapter_info.h"
#include "dorado_version.h"
#include "hts_utils/KString.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeli... |
45ec81b09ba9a1c56e0f9e94402b3f0126bc7dd7bf1f46d8554f7f068c6141a7 | C++ | 10,025 | 199 | #include "torch_utils/metal_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <torch/torch.h>
#include <cstdint>
#include <vector>
namespace {
using namespace dorado::utils;
// For convenient Slice syntax.
using namespace torch::indexing;
namespace F = torch::nn::functional;
#define TEST_GROUP "Metal: "
... |
b766eddda309904640e0814c9b97e8cdfdc41c536d08292f75f78606dd9f9014 | C++ | 10,074 | 198 | #include "api/pipeline_creation.h"
#include "basecall/ModelRunnerBase.h"
#include "config/BasecallModelConfig.h"
#include "modbase/ModBaseRunner.h"
#include "read_pipeline/nodes/BasecallerNode.h"
#include "read_pipeline/nodes/ModBaseCallerNode.h"
#include "read_pipeline/nodes/ModBaseChunkCallerNode.h"
#include "read_p... |
1a9b903e508b07aa926db1baa4acff25c67114cce455643bd58ecbffc6031cc1 | C++ | 10,138 | 260 | #include "MPSCaller.h"
#include "MetalCallerTask.h"
#include "basecall/crf_utils.h"
#include "decode/beam_search.h"
#include "model/TxModel.h"
#include "torch_utils/metal_utils.h"
#include "utils/memory_utils.h"
#include <spdlog/spdlog.h>
#include <cassert>
#include <cstdint>
#include <cstdlib>
#include <mutex>
#inc... |
edc90a5cf58764cf0f6c0e852b29a718e0c1a8efd0f9520f0066458d72b89831 | C++ | 10,280 | 296 | #include "bam_record_parsing.h"
#include "sequence_utility.h"
#include <htslib/sam.h>
#include <spdlog/fmt/bundled/format.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cassert>
#include <charconv>
#include <cstdio>
#ifdef NDEBUG
#define LOG_TRACE(...)
#else
#define LOG_TRACE(...) spdlog::trace(__VA_A... |
79653860a55958320ac0d78b68ae8326b8c18b2770247c9b7d047ef9f8154180 | C++ | 10,303 | 255 | #include "TestUtils.h"
#include "hts_utils/hts_types.h"
#include "secondary/common/vcf_writer.h"
#include <catch2/catch_approx.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_string.hpp>
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <cstdint>
#include <filesystem>
#inc... |
3c327ab956ab7d0bb4b0cf8b01fad7d95a88011d8f777bbc519473dadc458c8f | C++ | 10,307 | 225 | #include "models/metadata.h"
#include <catch2/catch_test_macros.hpp>
#include <set>
#include <stdexcept>
#define TEST_TAG "[ModelMetadata]"
using namespace dorado::models;
CATCH_TEST_CASE(TEST_TAG " ModelVariant enumeration", TEST_TAG) {
const auto& codes = model_variants_map();
CATCH_SECTION("Only expec... |
2cd5b08ab8d69238f229d992dd44ad4f17b9a0283c524baa66f0d879ee9c9b16 | C++ | 10,436 | 255 | #include "TestUtils.h"
#include "hts_utils/HeaderMapper.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 <catch2/catch_test_macros.hpp>
#include <htslib/sam.h>
#include <filesystem>
#include <numeric>
#include <optio... |
f015db27ef328f50f5de9d2ca05a38f1e94681bb33b1160c17e2c551aa7c48fa | C++ | 10,479 | 208 | #include "TestUtils.h"
#include "secondary/common/bam_file.h"
#include <catch2/catch_test_macros.hpp>
#include <iostream>
#include <string>
#include <vector>
namespace dorado::secondary::tests {
#define TEST_GROUP "[SecondaryBamFile]"
CATCH_TEST_CASE("Iterate over all BAM records", TEST_GROUP) {
const std::fi... |
315557a289fd031af54c3cd0359a1eb07636cc344bfab9f6929851cfc9e51254 | C++ | 10,490 | 192 | #include "models/kits.h"
#include "utils/string_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <set>
#define TEST_TAG "[ModelKits]"
using namespace dorado::models;
CATCH_TEST_CASE(TEST_TAG " FlowcellCode enumeration", TEST_TAG) {
const auto& fcs = flowcell_codes();
CATCH_SECTION("FlowcellCode t... |
547dbd8c49e687186105154656f26e917ec65c0005edbb4abed05631067b7a46 | C++ | 10,910 | 318 | #include "utils/ResourceLimiter.h"
#include "utils/concurrency/synchronisation.h"
#include "utils/jthread.h"
#include <catch2/benchmark/catch_benchmark.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <atomic>
#inc... |
6ee9bbbceb023449287a0eed2705ec55f1886a9861f471c01d1bd647846e09bd | C++ | 10,916 | 257 | #include "read_pipeline/nodes/AlignerNode.h"
#include "aligner/Minimap2Aligner.h"
#include "alignment/Minimap2Index.h"
#include "alignment/Minimap2MemoryLimiter.h"
#include "alignment/alignment_info.h"
#include "alignment/minimap2_args.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages... |
634445513b877f30e7a1120bc8774af2284bf8931f96266fd3a3126ca03fdf7f | C++ | 11,303 | 226 | #include "stereo_features.h"
#include "utils/sequence_utils.h"
#include <ATen/TensorIndexing.h>
#include <ATen/TensorOperators.h>
#include <algorithm>
#include <array>
#include <optional>
#include <vector>
using namespace at::indexing;
namespace dorado {
at::Tensor generate_stereo_features(const DuplexRead::Stere... |
3bf9f7acf59790a7e1b3c7a0350db1297e47298ec5762a36e33e369c2d6f3276 | C++ | 11,328 | 291 | #include "batchsize_benchmarks/batchsize_benchmarks.h"
#include "BenchmarkCache.h"
#include "BenchmarkSink.h"
#include "api/runner_creation.h"
#include "batchsize_helpers.h"
#include "config/BasecallModelConfig.h"
#include "data_loader/DataLoader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/... |
719989a749cf7133dbbae1b018723cb2717c6b6409d953e819b2608402b03998 | C++ | 11,441 | 247 | #include "nn/LSTMStack.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include <stdexcept>
#include <string>
#if DORADO_CUDA_BUILD
extern "C" {
#include "koi.h"
}
#endif
#include <torch/nn.h>
namespace dorado::nn {
LSTMStackImpl::LSTMStackImpl(int num_layers, int size, bool revers... |
7a2892ca1a540a71a53c6a7882960a87f69194f6d43ec7ee7b95f3cce507abc7 | C++ | 11,485 | 334 | #include "alignment/minimap2_args.h"
#include "alignment/minimap2_wrappers.h"
#include "utils/arg_parse_ext.h"
#include "utils/string_utils.h"
#include <argparse/argparse.hpp>
#include <minimap.h>
#include <mmpriv.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <stdexcept>
#include <string_view>
namespa... |
246d50b85c8d3534e2aea3a4b3a3b11848a3331e864a6000da7394f6609bd2b5 | C++ | 11,505 | 289 | #include "alignment/bed_file.h"
#include "TestUtils.h"
#include "utils/stream_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <sstream>
#include <string>
#define CUT_TAG "[dorado::alignment::BedFile]"
namespace dorado::alignment::bed_file::test {
namespa... |
cc52eb7e15c1965b93a50f9e9072f39c873db3f8b6787b7bfe4d20784c6af443 | C++ | 11,536 | 319 | #include "alignment/Minimap2Index.h"
#include "alignment/minimap2_wrappers.h"
#include "hts_utils/FastxSequentialReader.h"
#include "hts_utils/header_sq_record.h"
#include "hts_utils/hts_types.h"
#include "hts_utils/sequence_file_format.h"
#include <spdlog/spdlog.h>
//todo: mmpriv.h is a private header from mm2 for ... |
625e026c9c7409b6b44c90f535b22c5839ecbce045e487b7120bd7022f753521 | C++ | 11,656 | 312 | #include "splitter_utils.h"
#include <ATen/ops/from_blob.h>
#include <catch2/benchmark/catch_benchmark.hpp>
#include <catch2/catch_template_test_macros.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <spdlog/spdlog.h>
#include <limits>
#include <random>
#include... |
d0560fb7829ddf3b6bbf652466cb68834cd219b4e5aced11a5044ded5fadc0ea | C++ | 11,872 | 254 | #include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "read_pipeline/nodes/PairingNode.h"
#include "read_pipeline/nodes/ReadSplitNode.h"
#include "read_pipeline/nodes/StereoDuplexEncoderNode.h"
#include "read_... |
c502edd8d177a346c70c0470c8659c51050ae444c21bd16f9dcebbc5bedfa6e3 | C++ | 11,915 | 280 | #include "alignment/IndexFileAccess.h"
#include "TestUtils.h"
#include "alignment/Minimap2Index.h"
#include "alignment/minimap2_wrappers.h"
#include "utils/stream_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <filesystem>
#define TEST_GROUP "[alignment::IndexFileAccess]"
using namespace dorado::utils;
... |
ee25a8517a9fbe491a0bd4a24adfd344d3b8ff08988d78ab40bf9f1297ffe007 | C++ | 11,976 | 237 | #include "hts_utils/MergeHeaders.h"
#include "TestUtils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers.hpp>
#include <htslib/sam.h>
#include <stdexcept>
#define TEST_GROUP "[merge_headers]"
using namespace dorado;
using dorado::utils::MergeHeaders;
CATCH_TEST_CASE("MergeHeader... |
e91664a5b1de474c3d7a770986c9328fa3de4e7e73222a2c28bb300736f45ed0 | C++ | 11,978 | 305 | #include "alignment/sam_utils.h"
#include "utils/SeparatedStream.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <map>
#include <tuple>
#include <type_traits>
#include <unordered_map>
#include <utility>
namesp... |
51d2e3d75477611aedb7cc79129728e65461910113c2a4e626676841bee981d9 | C++ | 11,993 | 275 | #include "correct/windows.h"
#include "secondary/common/interval.h"
#include "utils/cigar.h"
#include "utils/overlap.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <cstdint>
#include <iostream>
#include <string>
#include <utility>
#include <vector>
#define TEST_... |
901e3487638c43cffd31dd629094627825aea1b3e2e9bb3296a4e568310f5289 | C++ | 12,041 | 307 | #include "models/model_complex.h"
#include "models/metadata.h"
#include "models/models.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <optional>
#include <stdexcept>
#include <vector>
namespace dorado::models {
ModelComplex::ModelComplex(const std::string& raw,
co... |
b181caf3d6cff3b0e643052f627ed99254c7e684e4ed0c22c9cd553b667c843b | C++ | 12,043 | 352 | /****************************************************************************
**
** Copyright (c) 2008-2018 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/Qhull.cpp#6 $$Change: 2549 $
** $DateTime: 2018/12/28 22:24:20 $$Author: bbarber $
**
**************************************************... |
1969ec52593e359d11f549539af282d10b628b86e704b77ee10f7bfd3ff74480 | C++ | 12,144 | 339 | #include "utils/AsyncQueue.h"
#include "utils/jthread.h"
#include <catch2/benchmark/catch_benchmark.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <spdlog/spdlog.h>
#include <atomic>
#include <chrono>
#include <latch>
#include <numeric>
#include <thread>
usin... |
7e535e83d13225e1622cda6d16f842641ea466633009ad03e695d7af7362b018 | C++ | 12,148 | 339 | #include "torch_utils/tensor_utils.h"
#include "utils/dev_utils.h"
#include "utils/simd.h"
#include <torch/serialize.h>
#include <cstddef>
#include <cstring>
#include <fstream>
#include <ostream>
#include <sstream>
#include <vector>
#ifndef NDEBUG
#include <spdlog/spdlog.h>
#endif
namespace dorado::utils {
namesp... |
8b4c0c2e3445ef253049286dab7e2e5ba36959fbbceffc36d64e613a955a4501 | C++ | 12,190 | 285 | #include "secondary/features/encoder_utils.h"
#include "secondary/features/medaka_read_matrix.h"
#include "torch_utils/tensor_utils.h"
#include "utils/container_utils.h"
#include <spdlog/spdlog.h>
#include <cstddef>
#include <span>
#include <unordered_map>
#include <unordered_set>
#ifdef NDEBUG
#define LOG_TRACE(..... |
0601e29350f573d5aea74b275339ab3e5492d53fde01cb06f88e2225e798d9f0 | C++ | 12,461 | 404 | #include <stdlib.h>
#include <iostream>
#include <stdio.h>
#include <unistd.h>
#include <sstream>
#include <mutex>
#include "sequence.h"
#include "global_parameter.h"
#include "read_filter.h"
using namespace::std;
C_single_fastq_filter::C_single_fastq_filter(C_fastq& a,C_global_parameter& gp){
read=a;
read_result=st... |
97c2df7d81b7e8bb7c1d3c807ff4e80f39973df0bbc63cd2e2aa38d203a20160 | C++ | 12,531 | 300 | #include "nn/FLSTMStack.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include <stdexcept>
#include <tuple>
#if DORADO_CUDA_BUILD
extern "C" {
#include "koi.h"
}
#endif
namespace dorado::nn {
FLSTMLayerImpl::FLSTMLayerImpl(const int C, const int K, at::TensorOptions opts) : C_(C... |
b74e9571b09975de9bf870e054f4ddf7030147458684d39b0932305c63232902 | C++ | 12,549 | 290 | #include "ProgressTracker.h"
#include "utils/string_utils.h"
#include "utils/tty_utils.h"
#include "utils/types.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <sstream>
#include <tuple>
#include <utility>
namespace dorado {
ProgressTracker::ProgressTracker(Mode mode, int total_reads)
: Progres... |
e9d42a8019d8af55559fd833fa2a177edac20c649f68941fe0cd047406dbc33f | C++ | 12,698 | 657 | // #include<iostream>
// #include<algorithm>
#include <string>
#include <vector>
#include <sstream>
#include <cctype>
#include <set>
#include <time.h>
#include <sstream>
#include <unistd.h>
#include <stdio.h>
#include <iostream>
#include <stdlib.h>
#include <sys/stat.h>
#include <algorithm>
#include <fstream>
#include ... |
08de5c9297a5f3fb6ea2dcf2c9fb24b0967c81bcf36dd9e3cfb791225ebf3522 | C++ | 12,748 | 307 | #include "alignment/Minimap2Index.h"
#include "TestUtils.h"
#include "alignment/minimap2_args.h"
#include "alignment/minimap2_wrappers.h"
#include "hts_utils/hts_file.h"
#include "read_pipeline/nodes/HtsWriterNode.h"
#include <catch2/benchmark/catch_benchmark.hpp>
#include <catch2/catch_test_macros.hpp>
#include <cat... |
5d2ac820e21e74d0c5813c5349928685bda4f107f6d18243287f055d5612453c | C++ | 12,850 | 292 | #include "read_pipeline/nodes/ScalerNode.h"
#include "config/BasecallModelConfig.h"
#include "demux/adapter_info.h"
#include "models/kits.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "torch_utils/tensor_utils.h"
#include "torch_utils/trim.h"
#include "util... |
1ded8c874c6cad33b56e28f8ed54b08035f2e5d7b476cb7a0d258e6d4b388ad3 | C++ | 13,223 | 310 | #include "model_latent_space_lstm.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include <cmath>
#include <stdexcept>
#include <unordered_map>
namespace dorado::secondary {
namespace {
enum class ActivationType {
RELU,
};
torch::nn::Sequential make_1d_conv_layers(const std::v... |
199357b8bc669713b0185820bf08a1e3dbe337cd7ac3c3ed95e7bf2cb4d7ae7a | C++ | 13,239 | 326 | #include "utils/sequence_utils.h"
#include <catch2/benchmark/catch_benchmark.hpp>
#include <catch2/catch_approx.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/internal/catch_run_context.hpp>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cstd... |
b3ac9d79b62e8e70ecb1e232344bc421eac7f73c34a2c93d16cae66da96e8141 | C++ | 13,253 | 288 | #include "read_pipeline/base/chunk.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <random>
#include <span>
#define TEST_GROUP "[utils]"
CATCH_TEST_CASE("Test generate_chunks", TEST_GROUP) {
CATCH_SECTION("Invalid input") {
auto [num_samples, chunk_s... |
50a66215ed3648e1856aed6670216315b9af768296c409992f2e782f0b7f277c | C++ | 13,328 | 335 | #include "file_info/file_info.h"
#include "utils/PostCondition.h"
#include "utils/fs_utils.h"
#include "utils/time_utils.h"
#include <pod5_format/c_api.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <iterator>
#include <set>
#include <stdexcept>
#include <string_view>
namespace {
using namespace std::l... |
bb349dcf44b5482794f1ba1f4d2e43e65c0e5633b24520bbe96f0ab23f720f14 | C++ | 13,398 | 308 | #include "read_pipeline/nodes/ModBaseChunkCallerNode.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
#include <cstdint>
#include <tuple>
#include <utility>
#define TEST_GROUP "[modbase_chunk]"
using namespace dorado::modb... |
dcf58e9d00f1ae98a6191e37276addd0c80c82b420a5f230970db2cc04f9c750 | C++ | 13,513 | 340 | #include "medaka_counts.h"
#include "medaka_bamiter.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <cassert>
#include <cerrno>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include <memory>
#include <ostream>
#include <stdexcept>
#include <unordered_set>
#define bam1_seq(b) ((b)->data + (b... |
bc07672635520d373b1ae30c5cd5dedd5bf3129d524dcf926aae65a541c69c6e | C++ | 13,730 | 377 | #include "hts_utils/MergeHeaders.h"
#include "hts_utils/KString.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/hts_types.h"
#include "utils/string_utils.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <iterator>
#include <limits>
#include <sstream>
#include <stdexcept>
n... |
6088c1f049342b4ee4c57a4b8f033c0db68ff9025149395df51c0399e869a09d | C++ | 13,753 | 320 | #include "TestUtils.h"
#include "hts_utils/fastq_tags.h"
#include <catch2/catch_test_macros.hpp>
#include <ostream>
#include <tuple>
namespace dorado::utils {
inline bool operator==(const dorado::utils::ReadGroupData& lhs,
const dorado::utils::ReadGroupData& rhs) {
return std::tie(lhs.fou... |
f2fe723dbf298cb36ac3327c0376f47553bb11368bd28b839bf94d2f82fb553d | C++ | 13,823 | 313 | #include "demux/parse_custom_kit.h"
#include "demux/parse_custom_sequences.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <toml.hpp>
#include <algorithm>
#include <optional>
#include <stdexcept>
#include <string>
#include <vector>
namespace {
const std::string ARRANGEMENT_TOML_KEY{"arrangement"};
co... |
8d4e18bfa082cb91583f7bc5d0e31f226ff037ece210beb00404ec017d899fd6 | C++ | 13,912 | 359 | #include "torch_utils/gpu_monitor.h"
#include <catch2/catch_test_macros.hpp>
#include <torch/torch.h>
#include <algorithm>
#include <cctype>
#include <sstream>
#define CUT_TAG "[dorado::utils::gpu_monitor]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
#define DEFINE_TEST_FIXTURE_METHOD(name) ... |
33a055cf5c8ef3db49500c992e9c832682e4c175a231ae2b854d5705de8a9a48 | C++ | 13,967 | 318 | #include "splitter_utils.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "read_pipeline/base/read_utils.h"
#include "utils/time_utils.h"
#include <ATen/TensorIndexing.h>
#include <bit>
#include <type_traits>
// MSVC doesn't define __SSE2__ so we have to do it ourselves.
#if defined(_M_AMD64)
#defin... |
327df4b1f23552c51a57a515aa04aad8fe1fcc242fa94619026bc48763f675c1 | C++ | 14,054 | 402 | #include "torch_utils/cuda_utils.h"
#include "torch_utils/gpu_monitor.h"
#include "utils/PostCondition.h"
#include "utils/math_utils.h"
#include <ATen/cuda/CUDAContext.h>
#include <ATen/ops/matmul.h>
#include <c10/cuda/CUDAGuard.h>
#include <cublas_v2.h>
#include <cuda_runtime.h>
#include <cuda_runtime_api.h>
#includ... |
253852c8f7f96d9706164b5d28371c3a0e6702c55f87cd000e2dce6ed0ff9f52 | C++ | 14,088 | 314 | #include "demux/Trimmer.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/messages.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "torch_utils/trim.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include "utils/types.h"
#include <ATen/TensorIndexing.h>
#include <hts... |
e0db5ac96800a24aa52d895f85f97528695f833743e75346096470c1607e870f | C++ | 14,221 | 325 | #include "flash_attention_module.h"
#include "flash_attention3_backend.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include <ATen/ops/scaled_dot_product_attention.h>
#include <c10/util/Exception.h>
#if DORADO_CUDA_BUILD
#include <ATen/cuda/CUDAContextLight.h>
#endif
#include <spdlo... |
c55b95a6364ed1c639691e0cfca9235955a546b9c893c134bb30b65f445dbdc4 | C++ | 14,293 | 354 | #include "kadayashi_utils.h"
#include "types.h"
#include <spdlog/spdlog.h>
#include <cassert>
#include <cstdlib>
#include <cstring>
#include <ctime>
#include <fstream>
#include <limits>
#include <sstream>
#ifdef NDEBUG
#define LOG_TRACE(...)
#else
#define LOG_TRACE(...) spdlog::trace(__VA_ARGS__)
#endif
namespace ... |
0f02d7949bac4af379f43c224e36a27b913ed0a663b8ca3634e86c313f7429d4 | C++ | 14,436 | 378 | #include "CorrectionMapper.h"
#include "aligner/Minimap2Aligner.h"
#include "alignment/Minimap2Index.h"
#include "alignment/Minimap2IndexSupportTypes.h"
#include "alignment/Minimap2Options.h"
#include "alignment/minimap2_args.h"
#include "alignment/minimap2_wrappers.h"
#include "hts_utils/bam_utils.h"
#include "read_p... |
6d3adf5f2549b7e8dee235e2f905e5d040998de48bd5a0cff849a57b38418ef6 | C++ | 14,555 | 412 | #include "utils/concurrency/AsyncExecutor.h"
#include "utils/concurrency/TaskPool.h"
#include "utils/concurrency/WorkerPool.h"
#include "utils/jthread.h"
#include <catch2/catch_template_test_macros.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <spdlog/spdlog.h>... |
0f17bb58272ba043c64f6e4e9bfa95c33c9c9077cee6d93d3d36b8c51525e423 | C++ | 14,797 | 303 | #include "modbase/encode_kmer.h"
#include "utils/sequence_utils.h"
#include "utils/simd.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <iterator>
#include <vector>
namespace {
// OneHot encoding encodes categorical data (bases... |
ac0a8390968e258c006f827a6f5983d99df7307ef736cc3a86c8ea7c558ffc80 | C++ | 14,831 | 352 | #include "adapter_primer_kits.h"
#include "demux/parse_custom_sequences.h"
#include "models/kits.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <cctype>
#include <set>
#include <sstream>
namespace dorado::adapter_primer_kits {
namespace {
// These HTS tags can be used in custom sequence fa... |
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