sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
81402953e56d465522f13bd664ead7d4d3e08c6f242e8ab803d12eb4560f2e66 | C++ | 3,468 | 98 | #include "SpeedEntry.h"
#include "csv_helpers.h"
#include "entries_equal.h"
#include <catch2/catch_test_macros.hpp>
#include <spdlog/spdlog.h>
#include <sstream>
#include <unordered_map>
#include <utility>
#define CUT_TAG "[batchsize_benchmarks]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
... |
99e5d489c0fe5825f77d6f8a1a119260874f0e18c62ec4cde4c2f2e1144c25b0 | C++ | 3,517 | 117 | #include "torch_utils/duplex_utils.h"
#include <ATen/TensorIndexing.h>
#include <ATen/TensorOperators.h>
#include <fstream>
#include <vector>
namespace dorado::utils {
std::map<std::string, std::string> load_pairs_file(const std::string& pairs_file_path) {
std::ifstream dataFile;
dataFile.open(pairs_file_pa... |
90392961c3050c1d66a12d4cb3e6811b15d1dc4e40bc63555e80bcc13e937495 | C++ | 3,594 | 102 | #include "utils/concurrency/TaskPool.h"
#include <cassert>
#include <chrono>
#include <thread>
namespace dorado::utils::concurrency {
namespace {
// How long to wait for a task on "our" queue when blocking.
constexpr auto kBlockingWaitFor = std::chrono::milliseconds(100);
// How many times to try and steal work fr... |
3297a57b69bc3b42a70932e868f4c303be9531ee9f84d54f5f57d0a64e569879 | C++ | 3,596 | 99 | #include "hts_utils/hts_types.h"
#include <htslib/sam.h>
#include <htslib/vcf.h>
#include <spdlog/spdlog.h>
#include <memory>
#include <sstream>
namespace dorado {
void BamDestructor::operator()(bam1_t* bam) { bam_destroy1(bam); }
void BcfHdrDestructor::operator()(bcf_hdr_t* header) {
if (header) {
bcf... |
81e10fe5d3f5a901af52b5ae3df1fb329a0a5e4ee618b78f080b8d103afb23aa | C++ | 3,616 | 111 | #include "utils/stats.h"
#include "utils/thread_utils.h"
#include <ostream>
#include <set>
namespace dorado::stats {
struct StatsSampler::StatsRecord {
int64_t elapsed_ms;
NamedStats stats;
};
StatsSampler::StatsSampler(std::chrono::system_clock::duration sampling_period,
std::ve... |
8a50111f44eb8e1f0742bdf097be57fd2db1248ea014c38081bec735c8b40c89 | C++ | 3,657 | 100 | #include "hts_utils/FastxRandomReader.h"
#include "TestUtils.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/hts_file.h"
#include "read_pipeline/nodes/HtsWriterNode.h"
#include <catch2/catch_test_macros.hpp>
#include <htslib/sam.h>
namespace {
using namespace dorado;
BamPtr generate_bam_entry(const std::st... |
40e75fe5c2bd17eafa240eead6b1eaf3896fa12f3b6f8a06e40d6046fd8ed338 | C++ | 3,667 | 103 | #include "model_downloader/model_downloader.h"
#include "downloader.h"
#include "models/models.h"
#include "utils/fs_utils.h"
#include <spdlog/spdlog.h>
#include <filesystem>
#include <vector>
namespace fs = std::filesystem;
namespace dorado::model_downloader {
bool download_models(const std::string& target_direc... |
4237adf3d2c6df3215c1280e2c7e4b12a2921c6acd09967302af5b8103405303 | C++ | 3,681 | 96 | #include "read_pipeline/nodes/ReadSplitNode.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "splitter/ReadSplitter.h"
#include <spdlog/spdlog.h>
#include <algorithm>
using namespace dorado::splitter;
namespace dorado {
namespace {
void validate_split_results(const std::vector<SimplexReadPtr>& sp... |
abe29ddef4bfba56ec4112b8082f7a208bc001c392c6a06ca3b023defaef3694 | C++ | 3,690 | 88 | #include "secondary/common/batching.h"
#include <stdexcept>
namespace dorado::secondary {
std::vector<Interval> compute_partitions(const int32_t num_items, const int32_t num_partitions) {
std::vector<Interval> chunks;
const int32_t chunk_size = num_items / num_partitions;
std::vector<int32_t> chunk_sizes... |
5ebd0245ac672aa2c3cdb69b2520657953476a6894414ff88d7386a1f9e858a3 | C++ | 3,701 | 103 | #include "alignment/Minimap2MemoryLimiter.h"
#include "utils/ResourceLimiter.h"
#include <minimap.h>
#include <spdlog/spdlog.h>
#include <memory>
namespace dorado::alignment {
namespace {
struct Limiters {
explicit Limiters(std::size_t big_queue_size, std::size_t small_queue_size)
: big_queue(big_... |
5deeb443143113cd0e352f2773f455a96f3ae887935c94c469a210a80d328b0e | C++ | 3,754 | 110 | #include "hts_utils/FastxRandomReader.h"
#include "hts_utils/sequence_file_format.h"
#include "utils/string_utils.h"
#include <htslib/faidx.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <memory>
namespace dorado::hts_io {
void FaidxDestructor::operator()(faidx_t* faidx) { fai_destroy(faidx); }
names... |
a09f0179b8a53dc4a7b2bd45db2cb6923dd340b7b0018fb11c8038220090c86e | C++ | 3,785 | 81 | #include "modbase/ModBaseContext.h"
#include <catch2/catch_test_macros.hpp>
#include <string>
#include <vector>
CATCH_TEST_CASE("basemod context helper encoding", "[bam]") {
dorado::modbase::ModBaseContext context_handler;
std::string expected_context = "_:XG:_:AXA"; // C has context CG, and T has context A... |
67bb0ae51aa4c0199f767f5de24f9dacc69cf8673ac89dbeacb84a8258593020 | C++ | 3,821 | 133 | #include "hts_utils/FastxSequentialReader.h"
#include "TestUtils.h"
#include <catch2/catch_test_macros.hpp>
#include <fstream>
namespace {
void write_lines(const std::filesystem::path& path, const std::vector<std::string>& lines) {
std::ofstream ofs(path);
bool first = true;
for (const std::string_view ... |
ad9d5fcb5c3fb5db00312119498e1113194ab5f6077fbea7b76fc2b9ddb0c3b6 | C++ | 3,902 | 92 | #include "basecall/CudaModelRunner.h"
#include "basecall/CudaCaller.h"
#include "torch_utils/cuda_utils.h"
#include "utils/math_utils.h"
#include <c10/cuda/CUDAGuard.h>
#include <sstream>
namespace dorado::basecall {
CudaModelRunner::CudaModelRunner(std::shared_ptr<CudaCaller> caller, size_t batch_dims_idx)
... |
b5f3afaca733d6db435c492d1ad37b4c1f34d34a7d6f76e71be6f4b712e5c81c | C++ | 3,924 | 119 | #include "utils/memory_utils.h"
#include <spdlog/spdlog.h>
#if defined(WIN32)
#include <windows.h>
#elif defined(__linux__)
#include <sys/sysinfo.h>
#elif defined(__APPLE__)
#include <mach/mach.h>
#include <sys/sysctl.h>
#endif
#include <array>
#include <fstream>
#include <sstream>
namespace dorado::utils {
double... |
fbd828f5868b62c3b2995d57d7b70dcc85595c63dca7e5253e36e0d609321cb2 | C++ | 3,946 | 105 | #include "ModBaseScaler.h"
#include "utils/math_utils.h"
#include <ATen/TensorOperators.h>
#include <nvtx3/nvtx3.hpp>
#include <algorithm>
#include <iterator>
#include <stdexcept>
namespace dorado::modbase {
ModBaseScaler::ModBaseScaler(const std::vector<float>& kmer_levels,
size_t kme... |
fac3e17a00d0be306e6f8d63089ad1a408d03ce188fca87f3d14d104d830a745 | C++ | 3,949 | 87 | #include "TestUtils.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/ReadPair.h"
#include "read_pipeline/nodes/StereoDuplexEncoderNode.h"
#include <catch2/catch_test_macros.hpp>
#include <torch/serialize.h>
#include <algorithm>
#include <filesystem>
#define TEST_GROUP "Ste... |
cbc55804fe167589e2409b82418228aa4131e25370d43edf377e4657f099650e | C++ | 3,964 | 131 | #include "utils/FunctionRef.h"
#include <catch2/catch_test_macros.hpp>
#include <functional>
#include <memory>
#include <type_traits>
#include <utility>
#define CUT_TAG "[FunctionRef]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
using namespace dorado::utils;
namespace {
template <typenam... |
9152eb61127b081721afd4f4a842636a7b98eb78c3cfe5a3d9174261e6de942f | C++ | 4,053 | 133 | #include "utils/crash_handlers.h"
#include <spdlog/spdlog.h>
#include <atomic>
#include <csignal>
#include <exception>
#ifdef _WIN32
// Reduce the impact of Windows.h
#define NOGDI
#define NOMINMAX
#define WIN32_LEAN_AND_MEAN
#include <Windows.h>
#endif
namespace dorado::utils {
namespace {
std::atomic_bool s_ena... |
2f41d8688ad3aab27c20fa257320f66e8f32eb9c29348163b7b297833a636288 | C++ | 4,089 | 111 | #include "nn/FactorisedLinearLayer.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#include <stdexcept>
#if DORADO_CUDA_BUILD
extern "C" {
#include "koi.h"
}
#endif
namespace dorado::nn {
FactorisedLinearLayerImpl::FactorisedLinearLayerImpl(int C_in, int K, int C_out)
: C_in... |
6fafdff10f8a5eebc924654d77567e514ca74d6e0c09a3adfc53f121e5570ea1 | C++ | 4,166 | 198 | /****************************************************************************
**
** Copyright (c) 2009-2018 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/Coordinates.cpp#6 $$Change: 2549 $
** $DateTime: 2018/12/28 22:24:20 $$Author: bbarber $
**
********************************************... |
6e1c084e89e182620d3502ae73cc92280079471368a4dab213d4d3009063abc3 | C++ | 4,177 | 118 | #include "config/BatchParams.h"
#include <spdlog/spdlog.h>
#include <toml.hpp>
#include <optional>
#include <stdexcept>
namespace dorado::config {
bool BatchParams::set_value(Value &self, const Value &other) {
if (other.priority != Priority::FORCE && other.priority <= self.priority) {
return false;
... |
4b512195a11e418ce35f8a60cf050dc499cec1b3c5504fa6ce8e21d6986e2b0d | C++ | 4,227 | 116 | #include "nn/WorkingMemory.h"
#include "utils/math_utils.h"
#include <ATen/ops/empty.h>
#include <c10/core/ScalarType.h>
#include <stdexcept>
namespace dorado::nn {
std::string to_string(const TensorLayout &layout) {
switch (layout) {
case TensorLayout::NTC:
return std::string("NTC");
case Tens... |
59a68cd760bb998d744d19328483b799341532775e0fb5c7f80b54d7310c3419 | C++ | 4,230 | 89 | #include "utils/time_utils.h"
#include <catch2/catch_message.hpp>
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <chrono>
#include <limits>
using std::make_tuple;
using namespace std::chrono;
using namespace std::chrono_literals;
#define CUT_TAG "[TimeUtils]"
CAT... |
79b0d7270edbff28b6d8356d1c7d3b137a5956e82dfd21e3c54d03b76c527544 | C++ | 4,237 | 123 | #include "secondary/common/variant.h"
#include "utils/container_utils.h"
#include <algorithm>
#include <ostream>
#include <string_view>
#include <tuple>
namespace dorado::secondary {
std::ostream& operator<<(std::ostream& os, const Variant& v) {
const auto print_map = [&os](const std::string_view name, const au... |
332da19f2ee31877db2ac21ec5e87b16d4c47fa9287303515d2fa3f82ca257dc | C++ | 4,292 | 108 | #include "hts_utils/fastq_tags.h"
#include "hts_utils/hts_types.h"
#include "utils/string_utils.h"
#if defined(__GNUC__) && !defined(__clang__) && !defined(__INTEL_COMPILER)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
#endif
#include <regex>
#if defined(__GNUC__) && !defined(__c... |
5a4e9e7313342602cd44ef8086356e6577e67cbe8a1f83271c6aa71ea5a001b8 | C++ | 4,301 | 104 | #include "read_pipeline/nodes/ReadToBamTypeNode.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/barcode_kits.h"
#include <spdlog/spdlog.h>
#include <algorithm>
namespace dorado {
void ReadToBamTypeNode::input_thread_fn() {
at::InferenceMode inference_mode_guard;
Message message;
... |
54e469ffa4b1c2ee7d003dad1c5e0d31d1cac80f499d47697be0cb215b860cf7 | C++ | 4,383 | 150 | #include "adjustwidget.h"
#include "ui_adjustwidget.h"
#include <QDebug>
#include <QListView>
#include <QLineEdit>
#include <QCollator>
AdjustWidget::AdjustWidget(QWidget *parent) :
QWidget(parent),
ui(new Ui::AdjustWidget)
{
ui->setupUi(this);
ui->comboBox_paramSelect->setView(new QListV... |
1b3d82767a212f0a8b2c1b33ec3e2f0486f6a694051f874c0ae57b030c81d4fb | C++ | 4,402 | 136 | #include "correct/decode.h"
#include "correct/conversions.h"
#include "correct/types.h"
#include <spdlog/spdlog.h>
#include <array>
#ifdef NDEBUG
#define LOG_TRACE(...)
#else
#define LOG_TRACE(...) spdlog::trace(__VA_ARGS__)
#endif
struct base_count_t {
int count = 0;
int base;
};
struct PairHash {
si... |
9075820e3177d06c07482bf86a6bf3f4e9eb9a7d5fa5a0b9b7a0c74dc8c3c435 | C++ | 4,459 | 126 | /**
* Helpers to interpose threading primitive methods in order to slow down
* execution and help TSan find issues that may otherwise be missed.
*/
#include "slow_interpose.h"
#include <dlfcn.h>
#include <atomic>
#include <cassert>
#include <thread>
#define CONCAT(a, b) a##b
#define STRINGIFY(x) #x
#define REAL_... |
52303b328af26192c5fc311fae8f20fe71c1ef55391397e64cd71983a6a065bf | C++ | 4,546 | 101 | #include "alignment/Minimap2Options.h"
#include "alignment/minimap2_args.h"
#include "alignment/minimap2_wrappers.h"
namespace dorado::alignment {
Minimap2IndexOptions::Minimap2IndexOptions() {
index_options = std::make_shared<Minimap2IdxOptHolder>();
}
Minimap2MappingOptions::Minimap2MappingOptions() {
map... |
f008840c8af150e45923cf9c5438cdda3a181ab9c14e2c02259f4bbef457c0fa | C++ | 4,587 | 134 |
#include "model_resolver/Models.h"
#include "config/BatchParams.h"
#include "utils/fs_utils.h"
#include <spdlog/spdlog.h>
#include <ranges>
namespace dorado::model_resolution {
Models::Models(ModelSources sources) : m_sources(std::move(sources)) {
m_simplex_config = config::load_model_config(m_sources.simplex... |
9245dfdb3723954c581b00cbc492689eb45663258c2f94bbc5d58b1f6e216971 | C++ | 4,592 | 124 | #include "cli/cli.h"
#include "cli/utils/cli_utils.h"
#include "dorado_version.h"
#include "hts_utils/HeaderMapper.h"
#include "hts_utils/hts_types.h"
#include "hts_writer/SummaryFileWriter.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/ReadInitialiser.h"
#include "read_pipeline/base/ReadPipe... |
04eecb77ab3083c55847bcd7de5f8d3df51ad4939347dc16107efd617353e652 | C++ | 4,639 | 162 | //
// Created by berry on 2020-10-09.
//
#include "BloomFilter.h"
#include <cstdint>
BloomFilter::BloomFilter(long long sampleSize, int multiple):multiple(20) {
if(sampleSize==0){
cerr<<"Error:no reads found in input file"<<endl;
exit(1);
}
hashNum=round(log(2)*multiple);
realUseBitSiz... |
342db2c008aa37643add1f38730c573f47f72aef73932cb28218e4ac6065c931 | C++ | 4,643 | 110 | #include "read_pipeline/base/stitch.h"
#include "read_pipeline/base/messages/ReadCommon.h"
#include "utils/math_utils.h"
#include "utils/string_utils.h"
#include <cassert>
#include <numeric>
#include <span>
namespace dorado::utils {
void stitch_chunks(ReadCommon& read_common, std::span<const Chunk*> called_chunks, ... |
fbf4dd929b68fe062952ef52868cfda53e677a45eeacf6c4cb0f7dadd7072b82 | C++ | 4,651 | 106 | #include "dna_poly_tail_calculator.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/PostCondition.h"
#include "utils/log_utils.h"
#include "utils/math_utils.h"
#include "utils/sequence_utils.h"
#include <edlib.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cmath>
#include <string... |
da16eb6dd143b77ccf99a9babd25c4c64cef3b71a53a8e211869225d2cf57345 | C++ | 4,683 | 118 | #include "CorrectionProgressTracker.h"
#include <spdlog/spdlog.h>
#include <algorithm>
namespace dorado {
CorrectionProgressTracker::CorrectionProgressTracker() {}
CorrectionProgressTracker::~CorrectionProgressTracker() = default;
void CorrectionProgressTracker::set_description(const std::string& desc) {
m_pr... |
4ce94a94c534b3715cc8695fe6cc7ac63e0d4347b64aa14584302f618fa38dac | C++ | 4,732 | 133 | #include "basecall_output_args.h"
#include "utils/string_utils.h"
#include <argparse/argparse.hpp>
#include <spdlog/spdlog.h>
#include <ctime>
#include <optional>
namespace dorado::cli {
namespace {
constexpr std::string_view OUTPUT_DIR_ARG{"--output-dir"};
constexpr std::string_view EMIT_FASTQ_ARG{"--emit-fastq"... |
a1e173d843c4459d1c1bb1e4e32f07ee9bd295b5e63b87001a73ad60db53043a | C++ | 4,756 | 112 | #include "TestUtils.h"
#include "file_info/file_info.h"
#include "utils/fs_utils.h"
#include "utils/stream_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
#include <stdexcept>
#define TEST_GROUP "[dorado::file_info]"... |
46e2575e0f10c7aa7e4a3441200462a7f12930653e67e67ca74a88dfe64f605c | C++ | 4,875 | 155 |
#include "utils/fs_utils.h"
#include <spdlog/spdlog.h>
#include <exception>
#include <filesystem>
#include <fstream>
#include <optional>
#include <random>
#include <set>
#include <sstream>
#include <stdexcept>
#include <string>
namespace fs = std::filesystem;
namespace dorado::utils {
std::string get_extension(co... |
0d51a7636fd789ecf47842514be53d26e9efbbebd8f4933b49b1e31421e20027 | C++ | 4,894 | 111 | #include "../dorado/secondary/architectures/model_variant_perceiver.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_string.hpp>
#include <torch/torch.h>
#include <stdexcept>
#include <vector>
namespace dorado::secondary::tests {
#define TEST_GROUP "[ModelVariantPerceiver]"
names... |
9eb595ff1c5bd521a23c75a78d27e5e66ac7592f26a66b34fa46ef37c41a49ef | C++ | 4,923 | 138 | #include "cli/cli.h"
#include "dorado_licences/licences.h"
#include "dorado_licences_pod5/licences.h"
#include "dorado_version.h"
#include "torch_utils/torch_utils.h"
#include "utils/crash_handlers.h"
#include "utils/locale_utils.h"
#include "utils/log_utils.h"
#include "utils/string_utils.h"
#include <minimap.h>
#inc... |
9705713380ac86cf0c3bb108305ada4609660d7f3af5920775bf7ebffa8e9131 | C++ | 4,932 | 124 | #include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <htslib/sam.h>
#include <filesystem>
#include <unordered_set>
#define ... |
c892a0cedfd7ed6b17893aa6ad94836d8791238932ffd8c41ae2d2f7d894d288 | C++ | 4,932 | 170 | #include "utils/SeparatedStream.h"
#include "catch2/catch_message.hpp"
#include "utils/string_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <optional>
#define TEST_GROUP "SeparatedStream"
#define DEFINE_TEST(name) CATCH_TEST_CASE(TEST_GROUP " : " name, T... |
81575102f278a5a5bf3b7d741e45a1a129e97c3632409632a0c254aa47291b54 | C++ | 4,971 | 144 | #include "utils/concurrency/WorkerPool.h"
#include "utils/concurrency/TaskPool.h"
#include "utils/hardware_interference_size.h"
#include "utils/thread_utils.h"
#include <spdlog/spdlog.h>
#include <cassert>
#include <stdexcept>
#include <thread>
namespace dorado::utils::concurrency {
struct alignas(hardware_destruc... |
cdfc304c7c8c814a222449e2acac5efd9a7bc2ea646e2148bdaa199e1c6be312 | C++ | 5,090 | 120 | #include "plasmid_poly_tail_calculator.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include <edlib.h>
#include <spdlog/spdlog.h>
namespace dorado::poly_tail {
namespace {
struct Result {
float score{-1.f};
int start{-1};
int end{... |
e82d8d56712b9f1f680f523707ebfc805a794fedbfe95cf7b87e8561f525be26 | C++ | 5,125 | 128 | #include "read_pipeline/nodes/PolyACalculatorNode.h"
#include "poly_tail/poly_tail_calculator.h"
#include "poly_tail/poly_tail_calculator_selector.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/context_container.h"
#include <spdlog/spdlog.h>
namespa... |
5e2fd8380445d5e2f23f95ee267ed8406b4140373ae140a85ce393b21f142da5 | C++ | 5,193 | 118 | #include "read_pipeline/nodes/DuplexReadTaggingNode.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <spdlog/spdlog.h>
namespace dorado {
void DuplexReadTaggingNode::input_thread_fn() {
at::InferenceMode inference_mode_guard;
Message message;
while (get_input_message(message)) {
... |
8a0bf7dd6b277a324e5ef8e07391da9bd6a0a2e9fb0a0671042686483ac83a32 | C++ | 5,229 | 167 | #include "secondary/common/bam_file.h"
#include "hts_utils/bam_utils.h"
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <stdexcept>
void HtsIdxDestructor::operator()(hts_idx_t* bam) { hts_idx_destroy(bam); }
void HtsItrDestructor::operator()(hts_itr_t* itr) const noexcept { hts_... |
3a9cf242b1bc3b5fa9972b107c7570e862c5b56559ca71c7619dcb1ec1a5452e | C++ | 5,241 | 136 | #include "splitter/RNAReadSplitter.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "splitter_utils.h"
#include "utils/log_utils.h"
#include "utils/uuid_utils.h"
#include <spdlog/spdlog.h>
#include <chrono>
#include <cmath>
#include <sstream>
#include <string>
using namespace dorado::splitter;
name... |
b74290106409135e9eeafc97f031f996a63898b356af194ed75a944f2dffed09 | C++ | 5,283 | 135 | #include "nn/CRFModules.h"
#include "nn/KoiUtils.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/tensor_utils.h"
#if DORADO_CUDA_BUILD
extern "C" {
#include "koi.h"
}
#endif
namespace dorado::nn {
LinearCRFImpl::LinearCRFImpl(int insize, int outsize, bool bias_, bool tanh_and_scale)
: bias(b... |
1e26666c97c6db7ce198ec7e10bc6c01725998af06fbf231b0f67dc59e76d4fd | C++ | 5,292 | 145 | #include "secondary/architectures/model_weights.h"
#include "torch_utils/tensor_utils.h"
#include "utils/container_utils.h"
#include <spdlog/spdlog.h>
#include <torch/csrc/autograd/InferenceMode.h>
#include <torch/serialize.h>
#include <fstream>
#include <stdexcept>
#include <vector>
namespace dorado::secondary {
n... |
4e3d4aed7c24b5527a423669a37b51643b3e031394027844af5444e745e1c712 | C++ | 5,308 | 155 | #include "BenchmarkCache.h"
#include "compiled_timings.h"
#include "csv_helpers.h"
#include "utils/string_utils.h"
#include <spdlog/spdlog.h>
#include <fstream>
#include <optional>
#include <string>
namespace dorado::batchsize_benchmarks {
namespace {
std::optional<std::string_view> get_gpu_name_alias(std::string... |
f65928449b2cc4e8aacb052632e1799ba05369d9cc7a1204c36b547f9735154a | C++ | 5,349 | 176 | #include "utils/MoveOnlyFunction.h"
#include <catch2/catch_test_macros.hpp>
#include <functional>
#include <memory>
#include <type_traits>
#include <utility>
#define CUT_TAG "[MoveOnlyFunction]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
using namespace dorado::utils;
namespace {
DEFINE_... |
853f332f13397826aba000e18ee5b4bc530934e508183cdf2a39d8be76520c0e | C++ | 5,356 | 146 | #include "read_pipeline/nodes/HtsWriterNode.h"
#include "utils/time_utils.h"
#include <htslib/bgzf.h>
#include <htslib/kroundup.h>
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <cassert>
#include <stdexcept>
namespace dorado {
using OutputMode = dorado::utils::HtsFile::OutputMode;
HtsWriterNode::Hts... |
4b99973877e1a7d9582e21b7628943a9d5cc5c13bf26d84c311de523d691b4a3 | C++ | 5,398 | 132 | #include "secondary/consensus/window_utils.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cmath>
#include <cstddef>
#include <iterator>
#include <stdexcept>
namespace dorado::secondary {
std::vector<Window> create_windows(const int32_t seq_id,
const int64_t seq_start... |
37f1f9712c3e61957ff17099d4cffb606c6cc784d2973c040bcc77129b5f9964 | C++ | 5,416 | 148 | #include "CRFModel.h"
#include "config/BasecallModelConfig.h"
#include "nn/FLSTMStack.h"
#include "nn/FactorisedLinearLayer.h"
#include "nn/KoiUtils.h"
#include "nn/LSTMStack.h"
#include "torch_utils/gpu_profiling.h"
#include "torch_utils/module_utils.h"
#include <optional>
#if DORADO_CUDA_BUILD
#include <ATen/cuda... |
c2a387573d65d05e56b3a8fffb72a6375124631365740621e867895c6b9e98a1 | C++ | 5,417 | 155 | #include "modbase/ModBaseContext.h"
#include "modbase/MotifMatcher.h"
#include "utils/sequence_utils.h"
#include <sstream>
namespace dorado::modbase {
ModBaseContext::ModBaseContext() {}
ModBaseContext::~ModBaseContext() {}
const std::string& ModBaseContext::motif(char base) const {
return m_motifs[utils::base... |
121c2c862ed98e63842a96069919291e2739aa03e381709487db2dd259574216 | C++ | 5,452 | 146 | #include "read_pipeline/nodes/SubreadTaggerNode.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/thread_utils.h"
#include <spdlog/spdlog.h>
namespace dorado {
void SubreadTaggerNode::input_thread_fn() {
at::InferenceMode inference_mode_g... |
2e6c886fa5f781eb0057ace5d23f507173c49d8f3b22345aa7f3fbb3e93511b2 | C++ | 5,512 | 140 | #include "modbase/ModBaseEncoder.h"
#include "modbase/encode_kmer.h"
#include "utils/sequence_utils.h"
#include <nvtx3/nvtx3.hpp>
#include <algorithm>
#include <cassert>
#include <cstdint>
#include <cstring>
#include <stdexcept>
namespace dorado::modbase {
ModBaseEncoder::ModBaseEncoder(size_t block_stride,
... |
6de38609fbef0d79316c331da2305fbabd08849c4b37de27f278256aed2ed127 | C++ | 5,567 | 161 |
#include "config/BatchParams.h"
#include "TestUtils.h"
#include "utils/parameters.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_all.hpp>
#include <optional>
#define CUT_TAG "[BatchParams]"
namespace fs = std::filesystem;
using dorado::config::BatchParams;
using dorado::utils:... |
7fb1cb2e3614410ab88c0cdc350d9975fa3af2f0d3efeadea7ef076341e136b7 | C++ | 5,589 | 146 | #include "alignment/IndexFileAccess.h"
#include "alignment/Minimap2Index.h"
#include <cassert>
#include <sstream>
namespace dorado::alignment {
const Minimap2Index* IndexFileAccess::get_compatible_index(
const std::string& index_file,
const Minimap2IndexOptions& indexing_options) {
auto& compati... |
80c5e30c872a5ce892851446132029fe4590eceb58b957940167a4d1ce56b5fb | C++ | 5,599 | 184 | #include "utils/FixedSizeQueue.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <memory>
#define TEST_GROUP "FixedSizeQueue"
#define DEFINE_TEST(name) CATCH_TEST_CASE(TEST_GROUP " : " name, TEST_GROUP)
using dorado::utils::FixedSizeQueue;
DEFINE_TEST("smoke test... |
25343f6a606bc5a5358523a7ce12ea012e518c333e4f9cba8358d227e2b01541 | C++ | 5,621 | 156 | #include "TestUtils.h"
#include "secondary/features/kadayashi_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <algorithm>
#include <cstdint>
#include <filesystem>
#include <fstream>
#include <sstream>
#include <unordered_map>
#include <vector>
namespace dorado::secondary::kadayashi_utils::tests {
#define ... |
141d178b700f227d5a0b375fce337e3e5f95f2ee2db00173acbee2054e1e06a0 | C++ | 5,712 | 128 | #include "rna_poly_tail_calculator.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/PostCondition.h"
#include "utils/log_utils.h"
#include "utils/math_utils.h"
#include "utils/sequence_utils.h"
#include <edlib.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cassert>
#include <cmat... |
cc48168af143ca26ba90e834ce36d2d8c7a431e339dfe0735c4b10734e1bcfc7 | C++ | 5,736 | 146 | #include "read_pipeline/base/ReadInitialiser.h"
#include "hts_utils/hts_types.h"
#include "utils/time_utils.h"
#include <catch2/catch_test_macros.hpp>
#include <htslib/sam.h>
#include <string>
#define TEST_GROUP "[read_pipeline][ReadInitialiser]"
namespace {
dorado::SamHdrPtr make_header() {
constexpr std::st... |
fa94b8b88f9e318220d0f3785c8c4cc2b41e33c6ac60913740bdf607da1e6f0b | C++ | 5,769 | 156 | #include "BenchmarkCache.h"
#include "SpeedEntry.h"
#include "TestUtils.h"
#include "entries_equal.h"
#include <catch2/catch_test_macros.hpp>
#define CUT_TAG "[batchsize_benchmarks]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " " name, CUT_TAG)
using namespace dorado::batchsize_benchmarks;
namespace {
DEFIN... |
3f82934e903c2cbd71b65af3ce796210e4cd6b8d4a9a1d62ac701e53d1b4e34e | C++ | 5,839 | 215 | //
// Created by berry on 2020-10-20.
//
#include "rmdup.h"
rmdup::rmdup(uint64_t* data, uint64_t size) {
this->data=data;
this->size=size;
}
void rmdup::markDup(bool *dupFlag) {
uint32_t prime=getPrime();
// cout<<get_local_time()<<"\tprime:\t"<<prime<<endl;
uint32_t *count=new uint32_t[prime];... |
b8e147e771108134860a9eb291b12ec1b9c08b7e8f684ade6620844372249235 | C++ | 5,872 | 158 | #include "CPUDecoder.h"
#include "beam_search.h"
#include "utils/thread_utils.h"
#include <ATen/TensorIndexing.h>
#include <ATen/TensorOperators.h>
#include <math.h>
#include <spdlog/spdlog.h>
#include <vector>
namespace {
// Operates in TNC
at::Tensor scan(const at::Tensor& Ms,
const float fixed_s... |
e86e641cfb64c875c70d7fd1a911cfd070e0e0d39685c9fb5c079e46110e8b5b | C++ | 5,901 | 138 | #include "secondary/common/bam_info.h"
#include "hts_utils/header_utils.h"
#include "secondary/common/bam_file.h"
#include "utils/container_utils.h"
#include "utils/string_utils.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <algorithm>
#include <stdexcept>
#include <unordered_map>
namespace dorado:... |
dcdc7f102fd997715cd5e49f3100637114606c1a2e8b3a4697312c67e9cd0e09 | C++ | 5,906 | 159 | #include "secondary/features/decoder_base.h"
#include "torch_utils/tensor_utils.h"
#include <cassert>
#include <cstdint>
#include <stdexcept>
namespace dorado::secondary {
DecoderBase::DecoderBase(const LabelSchemeType label_scheme_type)
: m_label_scheme_type(label_scheme_type) {}
std::vector<std::vector<s... |
814f8f42890752e54073221b1fa8b88f49ab3793d9d4a6aa7ff2b40a872cfe8e | C++ | 5,952 | 146 | #include "read_pipeline/nodes/PairingNode.h"
#include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "hts_utils/bam_utils.h"
#include "read_pipeline/base/DefaultClientInfo.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "utils/sequence_utils.h"
#include ... |
70e2510fd1f0525627faff679dd4f4de1aaeea841b597737f0fb7eafdd9b20ba | C++ | 5,988 | 169 | #include "secondary/common/region.h"
#include "utils/string_utils.h"
#include <IntervalTree.h>
#include <filesystem>
#include <fstream>
#include <ostream>
#include <sstream>
#include <stdexcept>
#include <tuple>
#include <unordered_map>
namespace dorado::secondary {
std::ostream& operator<<(std::ostream& os, const... |
1ed76eaec0ab48883dedc490287045c78d083acad2db14c6e2480da5d0c4fe33 | C++ | 6,000 | 157 | #include "modbase/ModBaseRunner.h"
#include "ModBaseScaler.h"
#include "config/ModBaseModelConfig.h"
#include "modbase/ModBaseCaller.h"
#include "torch_utils/tensor_utils.h"
#include <spdlog/spdlog.h>
#include <stdexcept>
#if DORADO_CUDA_BUILD
#include <c10/cuda/CUDAGuard.h>
#endif
namespace {
#if DORADO_CUDA_BUIL... |
c3b126c21b9e7e83398ec7ccfbc317f5f0910da4ec65ad8ffc93247069cf8b11 | C++ | 6,003 | 158 | #include "utils/concurrency/multi_queue_thread_pool.h"
#include "utils/thread_utils.h"
#include <algorithm>
namespace dorado::utils::concurrency {
MultiQueueThreadPool::MultiQueueThreadPool(std::size_t num_threads)
: m_num_threads{num_threads},
m_num_expansion_low_prio_threads(std::max(static_cast... |
f272b9ce4e0363cade1acded9a52512ba1c14df362217cabc8c7c5819cbf9fb1 | C++ | 6,028 | 134 | #include "MessageSinkUtils.h"
#include "TestUtils.h"
#include "data_loader/DataLoader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include <catch2/catch_test_macros.hpp>
#define TEST_GROUP "[dorado::DataLoader::pod5]"
CATCH_TEST_CASE(TEST_GROUP " Test loading ... |
4aaf6462f683d2d8d7c7bf2705866fdb1ac7044892a6e7b0cdc1229278f0f1bb | C++ | 6,209 | 176 | #include "utils/concurrency/multi_queue_thread_pool.h"
#include "utils/PostCondition.h"
#include "utils/concurrency/synchronisation.h"
#include <catch2/catch_test_macros.hpp>
#include <utility>
#define CUT_TAG "[dorado::utils::concurrency::MultiQueueThreadPool]"
#define DEFINE_TEST(name) CATCH_TEST_CASE(CUT_TAG " "... |
55baf7c3f5eac660156015faa350aa732649d95330b65b1853b71e11ff2829df | C++ | 6,212 | 131 | #include "secondary/features/encoder_factory.h"
#include "encoder_counts.h"
#include "encoder_read_alignment.h"
#include "secondary/architectures/model_config.h"
#include "secondary/architectures/model_config_validation.h"
#include <spdlog/spdlog.h>
#include <stdexcept>
#include <unordered_map>
namespace dorado::se... |
f50cbebc92adf7f86baf1b7495fe098c4cfb93881d46ff0bed6b926d8a9c72c5 | C++ | 6,270 | 183 | #include "secondary/architectures/model_config.h"
#include "secondary/architectures/model_config_validation.h"
#include <toml.hpp>
#include <cstddef>
#include <ostream>
#include <stdexcept>
namespace {
const std::string MODEL_TOML_KEY{"model"};
const std::string KWARGS_TOML_KEY{"kwargs"};
const std::string FEATURE_... |
7656f56780092329d9f0fc64afd47395ed3145c008fe35de70d3619f135a52fe | C++ | 6,272 | 162 | /* C file autogenerated by mexme.m */
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <stdlib.h>
#include <float.h>
#include <string.h>
/* Translate matlab types to C */
#define uint64 unsigned long int
#define int64 long int
#define uint32 unsigned int
#define int32 int
#define uint16 unsigned short
#... |
ee9b93c8cc37e4a171741d93c567edb88c5c20d054b793901c9aee530a799f72 | C++ | 6,273 | 159 | #include "poly_tail/poly_tail_config.h"
#include "utils/sequence_utils.h"
#include <toml.hpp>
#include <filesystem>
#include <fstream>
#include <istream>
#include <sstream>
#include <string>
#include <unordered_set>
namespace {
const std::string ANCHORS_TOML_KEY{"anchors"};
const std::string STATUS_TOML_KEY{"status... |
0fe934042afb1cdb32e04e75d7d1b72b646d5b60e8cfc4701b605e66228d4c50 | C++ | 6,280 | 162 | /* C file autogenerated by mexme.m */
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <stdlib.h>
#include <float.h>
#include <string.h>
/* Translate matlab types to C */
#define uint64 unsigned long int
#define int64 long int
#define uint32 unsigned int
#define int32 int
#define uint16 unsigned short
#... |
f1bd7f7a3307b57e6abe685c91889fc531f9f5af87231f5b32f0010512ac0a60 | C++ | 6,283 | 203 | #include "buttonstyle.h"
ButtonStyle::ButtonStyle()
{
}
/* ģʽÇл»°´Å¥Ñùʽ */
QString ButtonStyle::btModeInactiveStyle()
{
QString styleDescription =
"QPushButton {\
font-family: HarmonyOS Sans SC;\
border-radius: 15px;\
font:bold 32px;\
... |
9181a2c94182e32bcad536dab6585c326a18f6055bf71e937ec8a3dc85758466 | C++ | 6,328 | 207 | #include "utils/cigar.h"
#include "TestUtils.h"
#include <catch2/catch_test_macros.hpp>
#include <cstdint>
#include <filesystem>
#include <fstream>
#include <sstream>
#include <string>
#include <string_view>
#include <vector>
#define TEST_GROUP "[cigar]"
namespace dorado {
namespace cigartests {
CATCH_TEST_CASE("... |
61ada8432b1d7c31c08f4443a9b7dfbe2a076890036a6ef6bb52a7cbfc840c6b | C++ | 6,368 | 182 | #include "secondary/consensus/sample_collate_utils.h"
#include <ATen/ops/rand.h>
#include <catch2/catch_test_macros.hpp>
#include <cstdint>
#include <vector>
namespace dorado::secondary::sample_collate_utils::tests {
#define TEST_GROUP "[SecondaryConsensusSampleCollateUtils]"
namespace {
Sample create_mock_sample... |
26f87c4f99e1d44b1bf609bfa2a043855817b06199cf64d71095d20a20a4d3f6 | C++ | 6,386 | 138 | #include "read_pipeline/nodes/StereoDuplexEncoderNode.h"
#include "read_pipeline/base/messages/DuplexRead.h"
#include "read_pipeline/base/messages/ReadPair.h"
#include "utils/sequence_utils.h"
#include <ATen/ops/flip.h>
#include <edlib.h>
#include <cassert>
#include <cstring>
namespace dorado {
DuplexReadPtr Stere... |
05576ff8061b79191c47b973dd8bef1cee3a193e908a56ab669ccc03ddf4cb71 | C++ | 6,389 | 165 | #include "TestUtils.h"
#include "hts_utils/hts_file.h"
#include "read_pipeline/base/HtsReader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include "read_pipeline/nodes/HtsWriterNode.h"
#include "utils/stats.h"
#include <catch2/catch_test_macros.hpp>
#include <catch2/generators/catch_generators.hpp>
#include <catch... |
ebe6eafb6dc1cfcee1d63cef91e6c7f1ab9538905d7a0b7e9aabd49b9a713c78 | C++ | 6,394 | 178 | #include "models/metadata.h"
#include "utils/string_utils.h"
#include <algorithm>
#include <ostream>
#include <stdexcept>
#include <string>
namespace dorado::models {
namespace model_variant {
const std::unordered_map<std::string, ModelVariant> map = {
{"auto", ModelVariant::AUTO},
{"fast", ModelVar... |
76c68def1cbc4f6b53ba12509d6b982c04c507e52c071ecba34c32b5de965656 | C++ | 6,427 | 165 | #include "read_pipeline/base/ReadPipeline.h"
#include <spdlog/spdlog.h>
#include <algorithm>
#include <cctype>
#include <ranges>
using namespace std::chrono_literals;
namespace dorado {
// Depth first search that establishes a topological ordering for node destruction.
// Returns true if a cycle is found.
bool Pip... |
06ed728c6cc9e9ce09d80e492f1cecbba92c527ba91fd7a1d9b31c1250c4c140 | C++ | 6,454 | 158 | #include "nn/AuxiliaryData.h"
#include "nn/KoiThreads.h"
#include "utils/math_utils.h"
#include <ATen/ops/empty.h>
#include <ATen/ops/from_blob.h>
#include <ATen/ops/zeros.h>
#include <numeric>
#include <stdexcept>
#if DORADO_CUDA_BUILD
#include <c10/cuda/CUDAStream.h>
extern "C" {
#include "koi.h"
}
#endif
names... |
3fbe08965775acf538d6b21565d899a1c5d1a94c459d9f3195740db64ebd1536 | C++ | 6,475 | 155 | #include "read_pipeline/base/ReadInitialiser.h"
#include "hts_utils/KString.h"
#include "hts_utils/bam_utils.h"
#include "utils/barcode_kits.h"
#include "utils/time_utils.h"
#include <htslib/sam.h>
#include <iomanip>
#include <sstream>
namespace dorado {
namespace {
void assign_not_empty(std::string& attr_target,... |
9dbd4452f9492f68aedf28c867f0136b0d8105fe4e98df0656410f50721fe42b | C++ | 6,607 | 165 | #include "read_pipeline/nodes/TrimmerNode.h"
#include "demux/Trimmer.h"
#include "demux/adapter_info.h"
#include "demux/barcoding_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 "utils/con... |
9a6e80bd4288c077abfb3070d9fa8015d857a63623d7697d5092d408b87ba1c8 | C++ | 6,616 | 211 | #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:... |
41b2130f6c484504af84c0578645d6a8380c89883910219d839c022ca5a37615 | C++ | 6,628 | 168 | #include "read_pipeline/base/read_utils.h"
#include "read_pipeline/base/messages/SimplexRead.h"
#include "torch_utils/trim.h"
#include "utils/log_utils.h"
#include "utils/sequence_utils.h"
#include <ATen/TensorIndexing.h>
#include <spdlog/spdlog.h>
#include <cmath>
#include <cstdint>
using Slice = at::indexing::Sli... |
36d69aa266f68c1533e69bf1d2773a5cd6aab957d90f0fd14e4d4a7d98803037 | C++ | 6,629 | 170 | #include "splitter/myers.h"
#include "utils/PostCondition.h"
#include "utils/alignment_utils.h"
#include <algorithm>
#include <cassert>
#include <cstdint>
#include <iomanip>
#include <optional>
#include <ostream>
namespace dorado::splitter {
namespace {
// Returns the array D[0..n], where D[i] is equal to local al... |
8e27572c531446e10a7eaca99786fd4b03bbd6b1accd6be90564b14b7c458ccb | C++ | 6,704 | 152 | #include "read_pipeline/base/chunk.h"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <stdexcept>
#include <string>
namespace dorado::utils {
std::vector<std::size_t> generate_chunks(const std::size_t num_samples,
const std::size_t chunk_size,
... |
d29a4389353d00e476afc9d2bc110e9b21b36d95f6d66ee7ac85232d1a2cf48e | C++ | 6,730 | 162 | #include "hts_writer/HtsFileWriter.h"
#include "hts_utils/bam_utils.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "spdlog/fmt/bundled/format.h"
#include "utils/barcode_kits.h"
#include "utils/time_utils.h"
#include <htslib/sam.h>
#include <atomic>
#include <stdexcept>
namespace dorado... |
6a88cc25d3991f4c6cd369bc011cea0600f4ba5273fad0a106aef065cb3ced9f | C++ | 6,760 | 171 | /* C file autogenerated by mexme.m */
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <stdlib.h>
#include <float.h>
#include <string.h>
/* Translate matlab types to C */
#define uint64 unsigned long int
#define int64 long int
#define uint32 unsigned int
#define int32 int
#define uint16 unsigned short
#... |
53a408e2d4d5c6086671cb150a0a850cf7155f1f647bcba25cfffe2519064635 | C++ | 6,774 | 209 | #include "flash_attention3_backend.h"
#include <c10/util/Exception.h>
#include <spdlog/spdlog.h>
#include <mutex>
#include <optional>
#include <tuple>
#if DORADO_HAS_FLASHATTENTION3
#include <ATen/cuda/CUDAContextLight.h>
#include <flash_api.h>
#endif
namespace dorado::secondary {
namespace {
#if DORADO_HAS_FLASH... |
c31dde9f9ab800f6cab2edee208d7000281b449e4164ecca778a5fb1a3127480 | C++ | 6,774 | 182 | #include "hts_writer/Structure.h"
#include "hts_utils/hts_file.h"
#include "hts_utils/hts_types.h"
#include "hts_writer_utils.h"
#include "utils/barcode_kits.h"
#include "utils/time_utils.h"
#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <filesystem>
#include <sstream>
#include <stdexcept>
#include <str... |
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