sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ec4ddfdd74271de9b56208b1704d170e816557c987dd7e1a6105bdb3ad0ffd27 | C/C++ | 1,356 | 48 | #pragma once
#include <spdlog/spdlog.h>
namespace dorado::utils {
// Initialises the default logger to point to stderr.
void InitLogging();
enum class VerboseLogLevel : int {
none = 0,
debug = 1,
trace = 2,
};
void SetVerboseLogging(VerboseLogLevel level);
/// <summary>
/// Ensure a minimum logging lev... |
3bd17ab99db8f93d84190025177c4c83983879e0c25e5e9713b2df473e822635 | C/C++ | 1,363 | 32 | #pragma once
#include <cstdint>
#include <utility>
#include <vector>
namespace dorado::utils {
// Create overlapping (== overlap) chunks of equal length (== chunk_size) and return begin
// positions, where the last chunk pair will have a bigger overlap.
//
std::vector<std::size_t> generate_chunks(std::size_t num_sam... |
1c3cc625cf92a2f09a95cd2cddce97323bfe3371072315057c4f64544c8771a9 | C/C++ | 1,381 | 49 | #ifndef _INCLUDE_EVENT_H_
#define _INCLUDE_EVENT_H_
#include <stdbool.h>
#define EVENT_HEAD 0x78A2
/* ʼþÀàÐÍ */
typedef enum {
EVENT_CONNECT = (unsigned short)0x4121,
EVENT_START = (unsigned short)0x5214,
EVENT_STOP = (unsigned short)0x7521,... |
4d5011d1a9502c18530b48cda4ccc4db2696778bfa0efdcb4758fbbafebb0340 | C/C++ | 1,394 | 59 | #pragma once
#include <cmath>
#include <string>
#include <vector>
// Forward declaration of toml::value taken from toml_fwd.hpp
namespace toml {
template <typename TypeConfig>
class basic_value;
struct type_config;
using value = basic_value<type_config>;
} // namespace toml
namespace dorado::config {
// Activatio... |
b403464706ddc362a168c5924a68703e2225a43e7e1c256806ac53f8929761c0 | C/C++ | 1,412 | 39 | #pragma once
#include <iosfwd>
#include <string>
#include <vector>
namespace dorado::poly_tail {
struct PolyTailConfig {
std::string rna_adapter = "GGTTGTTTCTGTTGGTGCTG"; // RNA
std::string front_primer = "TTTCTGTTGGTGCTGATATTGCTTT"; // SSP
std::str... |
ed48d8ea7ebadd3bd6130abec83637ac3c73267a76d330391f7a7d3d7752c761 | C/C++ | 1,414 | 54 | #pragma once
#include <cstddef>
#include <memory>
#include <string_view>
namespace dorado::utils::concurrency {
class TaskPool;
// These are the threads that will execute the tasks.
class WorkerPool {
struct WorkerState;
const std::unique_ptr<WorkerState[]> m_states;
const std::size_t m_num_workers;
pr... |
313a07f2213025edfb7604e45b473b7a2ff54d3d037a6721a21c170fb9e28b7e | C/C++ | 1,426 | 46 | #pragma once
#include <map>
#include <mutex>
#include <optional>
#include <string>
#include <unordered_map>
#include <utility>
#include <vector>
namespace dorado::basecall {
class ChunkBenchmarks final {
public:
using ChunkTimings = std::unordered_map<int, float>;
using ModelName = std::string;
using GPU... |
e8254ec64339a33dc13e5a68d6b804b3e31728f0d8fe2c6aaf5706a7be1fedba | C/C++ | 1,434 | 50 | #pragma once
#include "demux/BarcodeClassifierSelector.h"
#include "read_pipeline/base/MessageSink.h"
#include "utils/concurrency/AsyncExecutor.h"
#include <atomic>
#include <map>
#include <mutex>
#include <string>
namespace dorado {
namespace demux {
struct BarcodingInfo;
}
class BarcodeClassifierNode : public Me... |
5078f8e7e14f2c9113f969aa55bd14007b28f7b2e49ec7ccc7d5792b3163abbe | C/C++ | 1,445 | 61 | #ifndef EVENT_H
#define EVENT_H
#include <QByteArray>
#define EVENT_HEAD 0x78A2
typedef enum {
EVENT_CONNECT = (unsigned short)0x4121,
EVENT_START = (unsigned short)0x5214,
EVENT_STOP = (unsigned short)0x7521,
EVENT_ERROR ... |
15b4b242823e3df7dacd8423c5154bcf392430e9e33bff639f48a7f701e33657 | C/C++ | 1,451 | 51 | #pragma once
#include "ModelRunnerBase.h"
#include <ATen/core/TensorBody.h>
#include <c10/cuda/CUDAStream.h>
#include <atomic>
#include <filesystem>
#include <memory>
#include <tuple>
#include <vector>
namespace dorado::basecall {
class CudaCaller;
class CudaModelRunner final : public ModelRunnerBase {
public:
... |
ae726ce61e4b8d16aed033332014c0017a6ad964e419382fc54516e2f272032e | C/C++ | 1,456 | 57 | #pragma once
#include "cigar.h"
#include <iosfwd>
#include <string>
#include <string_view>
#include <vector>
namespace dorado::utils {
struct Overlap;
struct PafEntry {
std::string qname{"*"};
int qlen = 0;
int qstart = 0;
int qend = 0;
char strand{'*'};
std::string tname{"*"};
int tlen... |
3faa680872cf6eeb90bd98f1c4fc42c75c213f657ed18e0b506ac7db7becb7bf | C/C++ | 1,458 | 43 | /**
******************************************************************************
* @file usbd_cdc_if_template.h
* @author MCD Application Team
* @brief Header for usbd_cdc_if_template.c file.
******************************************************************************
* @attention
*
* ... |
a6e225079228a55ff0077477bf7d7d0b2c74e9b8d2441c659dee522da745b663 | C/C++ | 1,461 | 48 | #pragma once
#include "ReadCommon.h"
#include <atomic>
#include <cstdint>
#include <limits>
#include <memory>
#include <string>
namespace dorado {
// Class representing a simplex read, including raw data
class SimplexRead {
public:
ReadCommon read_common;
float digitisation; // Loaded from source file
... |
73a13a566fa6c64ffa9eeed17d6ea6ad18b47bd08ea5861b4371388e0bad1ec8 | C/C++ | 1,463 | 47 | #pragma once
#include "ModelRunnerBase.h"
#include "config/BasecallModelConfig.h"
#include "utils/stats.h"
#include <torch/nn.h>
#include <atomic>
#include <string>
namespace dorado::basecall::decode {
class Decoder;
} // namespace dorado::basecall::decode
namespace dorado::basecall {
class ModelRunner final : p... |
53dc01aefc071c6e7270ba8dcbec0643636213f8771197a96529dc4678e2b79b | C/C++ | 1,480 | 47 | #pragma once
#include "splitter/ReadSplitter.h"
#include <ATen/core/TensorBody.h>
#include <algorithm>
#include <cassert>
#include <cstdint>
#include <optional>
namespace dorado::splitter {
template <class FilterF>
auto filter_ranges(const PosRanges& ranges, FilterF filter_f) {
PosRanges filtered;
std::cop... |
862c7a8708f8511cce93a38641b38f682b353b4fd291ad3b1864b0c85e01548b | C/C++ | 1,482 | 33 | #ifndef NEON_SSE_H
#define NEON_SSE_H
#include <arm_neon.h>
typedef uint8x16_t __m128i;
static inline __m128i _mm_load_si128(const __m128i *ptr) { return vld1q_u8((const uint8_t *) ptr); }
static inline __m128i _mm_set1_epi32(int n) { return vreinterpretq_u8_s32(vdupq_n_s32(n)); }
static inline void _mm_store_si128(... |
7b374ad4d44141e621b194d1f87504670c591dd64fdbebe3b5d09273eaff58fe | C/C++ | 1,487 | 59 | #pragma once
#include "RNNStack.h"
#include <torch/nn.h>
#include <vector>
namespace dorado::nn {
struct FLSTMLayerImpl : torch::nn::Module {
FLSTMLayerImpl(int C, int K, at::TensorOptions opts);
at::Tensor forward(at::Tensor x);
private:
int C_;
at::Tensor dn_weight_ih_;
at::Tensor dn_weight... |
37d6adb13b43379d355621d199f036c80acb08942ad14f295f0030fbca3c54b1 | C/C++ | 1,489 | 32 | #pragma once
#include "utils/MoveOnlyFunction.h"
namespace dorado::utils::concurrency {
//
// Rough overview:
// * Fixed number of persistent workers, held by WorkerPool.
// * TaskPools are (re)created and attached to the WorkerPool when pipelines are (re)created.
// * Fixed number of producers, one per node t... |
223dbbad3f001461ee9521f563a95b7cdcf48911bea4edc0eda84d18c6264c3d | C/C++ | 1,496 | 42 | #pragma once
#include "api/caller_creation.h"
#include "basecall/ModelRunnerBase.h"
#include "modbase/ModBaseRunner.h"
#include <filesystem>
#include <memory>
#include <span>
#include <string>
#include <utility>
#include <vector>
namespace dorado::api {
bool check_variable_chunk_sizes_supported(const config::Baseca... |
8012f6d22b6cfda3616169b74bdac73d290a4da5746370853cbb7df58a7a4329 | C/C++ | 1,501 | 56 | #pragma once
#include <ostream>
#include <sstream>
#include <string>
#include <vector>
namespace dorado::utils {
/**
* \brief Prints the contents of an iterable container to a stream. Useful for debug purposes.
*/
template <typename T>
void print_container(std::ostream& os,
const T& data,
... |
d0bc78b48d5220a65ec77d12265575961a1701a2022b71a4370fe2ae30b9a6ba | C/C++ | 1,507 | 53 | #pragma once
#include "utils/tty_utils.h"
#ifdef _WIN32
#include <indicators/progress_bar.hpp>
#else
#include <indicators/block_progress_bar.hpp>
#endif
namespace dorado {
#ifdef _WIN32
using ProgressBarBase = indicators::ProgressBar;
#else
using ProgressBarBase = indicators::BlockProgressBar;
#endif
class SimpleP... |
a30662f7cf30aca4bef848faa9740c5b34e04fcceffaea9fd41e0e203c147ed1 | C/C++ | 1,517 | 55 | #pragma once
#include <cstring>
#include <filesystem>
#include <string>
#include <vector>
namespace dorado::tests {
std::filesystem::path get_data_dir(const std::string& sub_dir);
// Reads into a string.
std::string ReadFileIntoString(const std::filesystem::path& path);
// Reads into a vector<uint8_t>.
std::vector... |
a6d5d00db37e3534f3a4e78133a10b917da0525a884ae67be81011227da808d1 | C/C++ | 1,520 | 72 | #pragma once
#include "hts_utils/hts_types.h"
#include "secondary/common/alignment.h"
#include <filesystem>
#include <string>
#include <vector>
struct htsFile;
struct hts_idx_t;
struct sam_hdr_t;
struct bam1_t;
struct hts_itr_t;
struct HtsIdxDestructor {
void operator()(hts_idx_t*);
};
using HtsIdxPtr = std::un... |
3adcb1e6db47368d0136049ea88fc74d377475cf047d6b279764feb75956cd05 | C/C++ | 1,524 | 69 | #ifndef LH3_BWTSW2_H
#define LH3_BWTSW2_H
#include <stdint.h>
#include "bntseq.h"
#include "bwt_lite.h"
#include "bwt.h"
#define BSW2_FLAG_MATESW 0x100
#define BSW2_FLAG_TANDEM 0x200
#define BSW2_FLAG_MOVED 0x400
#define BSW2_FLAG_RESCUED 0x800
typedef struct {
int skip_sw:8, cpy_cmt:8, hard_clip:16;
int a, b,... |
e7a12221907c494d3589587a24940c12d6b175443f7ca1040be0f76f06637775 | C/C++ | 1,539 | 61 | #pragma once
#include "dorado_version.h"
#include <cmath>
#include <cstdint>
#include <stdexcept>
#include <string>
#include <vector>
namespace dorado::utils::arg_parse {
inline bool parse_yes_or_no(const std::string& str) {
if (str == "yes" || str == "y") {
return true;
}
if (str == "no" || str... |
e6f8dc3b9f754bd12e3f79c13aeb29994c0f327c033b3cde6f78bed781a4dd8b | C/C++ | 1,548 | 58 | #ifndef ROPE_H_
#define ROPE_H_
#include <stdint.h>
#include <stdio.h>
#define ROPE_MAX_DEPTH 80
#define ROPE_DEF_MAX_NODES 64
#define ROPE_DEF_BLOCK_LEN 512
typedef struct rpnode_s {
struct rpnode_s *p; // child; at the bottom level, $p points to a string with the first 2 bytes giving the number of runs (#runs)
u... |
6ee72eb08ce53f83cfff8f8f9203730e7f38716a4de53deadf1193d21d4a2358 | C/C++ | 1,549 | 64 | #ifndef ADJUSTWIDGET_H
#define ADJUSTWIDGET_H
#include <QWidget>
#include <QStringList>
#include <QIntValidator>
namespace Ui {
class AdjustWidget;
}
enum AdjustWidgetEvent{
ADJUST_EVENT_REDUCE,
ADJUST_EVENT_ADD,
ADJUST_EVENT_EDIT_COMPLETED,
};
class AdjustWidget : public QWidget
{... |
b37ee4147b43ea6ba89d646a847be24988a667b2bf9313699ec7c6adeea92be8 | C/C++ | 1,563 | 69 | #ifndef MAINWIDGET_H
#define MAINWIDGET_H
#include "channelselectlayout.h"
#include "controldialog.h"
#include "hardwarethread.h"
#include "plotdialog.h"
#include <QProgressDialog>
#include <QWidget>
QT_BEGIN_NAMESPACE
namespace Ui { class MainWidget; }
QT_END_NAMESPACE
#define MAX_ROW 400
#define M... |
de64e5aa0a606d9ede8abde857d1f1b042d1808ad264329ade76010c8a2e8994 | C/C++ | 1,563 | 52 | #pragma once
#include "DecodedChunk.h"
#include "utils/stats.h"
#include <string>
#include <utility>
#include <vector>
namespace at {
class Tensor;
}
namespace dorado::config {
struct BasecallModelConfig;
} // namespace dorado::config
namespace dorado::basecall {
class ModelRunnerBase {
public:
virtual ~Mode... |
c72feb8580d9b61914853abf6348598110f0ed03d29b27f4935bdcb043e97383 | C/C++ | 1,569 | 54 | #pragma once
#include "read_pipeline/base/MessageSink.h"
#include <atomic>
#include <condition_variable>
#include <cstdint>
#include <mutex>
#include <thread>
#include <unordered_map>
#include <unordered_set>
#include <utility>
#include <vector>
namespace dorado {
class SubreadTaggerNode : public MessageSink {
publ... |
c70d8cb1bbc1e80f1bb55fe5fc1fcb4a75436c964f3bac9db98a7582d8e350b3 | C/C++ | 1,591 | 42 | #pragma once
#include "ReadSplitter.h"
#include <optional>
#include <vector>
namespace dorado::splitter {
class DuplexReadSplitter : public ReadSplitter {
public:
DuplexReadSplitter(DuplexSplitSettings settings);
~DuplexReadSplitter();
std::vector<SimplexReadPtr> split(SimplexReadPtr init_read) const ov... |
9e892d8478c170b988761bdabda0c68e4a3fb7771a84622c54a95bb17c4f6dbb | C/C++ | 1,608 | 46 | #pragma once
#include <chrono>
#include <cstdint>
namespace dorado {
namespace timer {
/// \brief Minimal timer object to facilitate recording time spans using the high resolution clock.
/// Starts a clock when constructed.
class TimerHighRes {
public:
TimerHighRes() : m_start_time(get_current_time()) {... |
59da8cfaeb218058954a5fcc09d684f6b98b27e8776edca825e8c92c76562539 | C/C++ | 1,646 | 45 | /* QSufSort.h
Header file for QSufSort.c
This file contains an implementation of the algorithm presented in "Faster
Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
Sadakane (sada@is.s.u-tokyo.ac.jp).
This software may be used freely for any purpose. However, when distributed,
t... |
01fb530f48a67f49fde94b669336ccc9215dcd398429ff4c137da55ed536f0ad | C/C++ | 1,728 | 46 | #pragma once
#include "consensus_result.h"
#include <cstdint>
#include <iosfwd>
#include <optional>
#include <string>
#include <string_view>
#include <unordered_set>
#include <vector>
namespace dorado::secondary {
std::string extract_draft_with_gaps(const std::string_view draft,
... |
205132a18619430ca5dae8c6ff0552554127f3f3521464dd0d6ca17701e1f1c3 | C/C++ | 1,781 | 58 | #pragma once
#include "hts_utils/HeaderMapper.h"
#include "hts_utils/hts_types.h"
#include "interface.h"
#include <filesystem>
#include <fstream>
#include <iosfwd>
#include <memory>
#include <string>
struct sam_hdr_t;
namespace dorado {
class HtsData;
namespace hts_writer {
class SummaryFileWriter : public IWrite... |
816b5a124f2ffec924fb1776fcc2cc7a33948d6b3149a530b95eb53fcdca34c3 | C/C++ | 1,806 | 57 | #ifndef GC_H
#define GC_H
#include <string>
#include <string.h>
#include <vector>
#include <sstream>
#include <cctype>
#include <set>
#include <map>
#include <math.h>
using namespace ::std;
class quartile_result
{
public:
float mean;
float median;
float lower_quar, upper_quar;
float first10_quar, last10_quar;
};
... |
fd985ab8f46d1d33071d46d7a8ea6dc623031f2a4930e6b77446f257035dd992 | C/C++ | 1,844 | 61 | #pragma once
#include "secondary/architectures/model_config.h"
#include <toml.hpp>
#include <cstdint>
#include <limits>
#include <string>
#include <unordered_map>
namespace dorado::secondary {
constexpr int32_t MODEL_CONFIG_MAX_VERSION = std::numeric_limits<int32_t>::max();
enum class ModelConfigValueType {
A... |
8a10dd1ad032edf904554ebdbd204e2339432440fc5df670945fbfca12039f20 | C/C++ | 1,910 | 77 | #ifndef RLE6_H_
#define RLE6_H_
#include <stdint.h>
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x),1)
#else
#define LIKELY(x) (x)
#endif
#ifdef __cplusplus
extern "C" {
#endif
int rle_insert_cached(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t ec[6], int *beg, int64_t bc[6]);
... |
4b648d6d66fa8ddf3b37872b232a0d77f368ac3df06a8044d41984f8151299b1 | C/C++ | 1,945 | 65 | #pragma once
#include "config/BasecallModelConfig.h"
#include "config/ModBaseModelConfig.h"
#include "model_resolver/ModelSources.h"
#include <filesystem>
#include <string>
#include <vector>
namespace dorado::model_resolution {
class Models {
public:
Models(ModelSources sources);
Models(const Models&) = del... |
c827ef0cd17f32e05ff4d17c2c90ea502bc8951b283c1a2932fbf7f86db655a5 | C/C++ | 1,957 | 67 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file stm32f4xx_it.h
* @brief This file contains the headers of the interrupt handlers.
******************************************************************************
* @attention
*
... |
3dd52858b41d9090ac4a94a9e87e0c4826de61560404b324228eb3371d1bbc98 | C/C++ | 1,972 | 68 | #pragma once
#include <condition_variable>
#include <cstdint>
#include <cstdlib>
#include <mutex>
#include <queue>
namespace dorado::utils {
// Class to limit access to a resource.
// Similar to a counting semaphore but with ordering.
class ResourceLimiter {
public:
// Note: instances of this should be thread_lo... |
47a5fa0db6a5aa05f45a53ca7d256794181873def72b76da3be7dc146b2ca068 | C/C++ | 1,974 | 68 | #pragma once
#include "utils/cigar.h"
#include "utils/overlap.h"
#include <cstdint>
#include <memory>
#include <string>
#include <vector>
namespace dorado {
// Overlaps for error correction
struct CorrectionAlignments {
// Populated in CorrectionMapperNode::extract_alignments
std::string read_name;
std:... |
d91ed2d2c46474e6610a20711ecdc337270def572924a26f820d0b1c8f386b6b | C/C++ | 1,980 | 54 | #pragma once
#include "alignment/Minimap2Index.h"
#include "hts_utils/hts_types.h"
#include "read_pipeline/base/messages.h"
#include "utils/types.h"
#include <minimap.h>
#include <memory>
#include <string>
#include <vector>
namespace dorado::alignment {
// Exposed for testability
extern const std::string UNMAPPED_... |
388d6701e0d2995d2eac223cd7f9c6394fd4b25063db69d78bea38fe4a78bbd9 | C/C++ | 1,983 | 63 | #pragma once
#include "multi_queue_thread_pool.h"
#include "synchronisation.h"
#include <condition_variable>
#include <memory>
#include <mutex>
#include <thread>
#include <type_traits>
namespace dorado::utils::concurrency {
// Executor for posting tasks to an underlying thread pool
//
// N.B. The executor itself is... |
2d7c36855d3f34465667864ab160c9b3650aa02227fa2b54bc1701998d1e1c8b | C/C++ | 1,988 | 58 | #pragma once
#include "AuxiliaryData.h"
#include "WorkingMemory.h"
#include "config/common.h"
#include <torch/nn.h>
#include <optional>
#include <vector>
namespace dorado::nn {
struct ConvStackImpl : torch::nn::Module {
explicit ConvStackImpl(const std::vector<config::ConvParams> &layer_params);
#if DORADO_CUD... |
5cfb006a6c81d5bd79c2faf5d7ceb90d5e53b8939c94ce84b10af211a0dcc3dc | C/C++ | 1,997 | 61 | #pragma once
#include <cstddef>
#include <memory>
struct kstring_t;
namespace dorado {
/// Wrapper for htslib kstring_t struct.
class KString {
public:
/** Contains an uninitialized kstring_t.
* Useful for later assigning to a kstring_t returned by an htslib
* API function. If you need to pa... |
c166006f65ac19d8fe4324d2e04c12912a6ce00d582503cb04d7b45482d27cd3 | C/C++ | 2,045 | 70 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : main.h
* @brief : Header for main.c file.
* This file contains the common defines of the application.
*******************************************... |
5ef5d5d4fb6f7df8f4077b9f99839f66dd055e3152d750defa80c8abdeb77edf | C/C++ | 2,061 | 59 | #pragma once
#include <filesystem>
#include <optional>
#include <set>
#include <string>
#include <string_view>
#include <vector>
namespace dorado::models {
struct ModelInfo;
}
namespace httplib {
class Client;
} // namespace httplib
namespace dorado::model_downloader {
using namespace models;
bool download_model... |
3bcea582c1d4518b3c7c4d90fc89b98ea960294af1334b8058556610ad985a3b | C/C++ | 2,083 | 66 | #pragma once
#include <cstdint>
#include <iosfwd>
#include <string>
#include <utility>
#include <vector>
namespace dorado::secondary {
struct RegionInt {
int32_t seq_id = -1;
int64_t start = 0;
int64_t end = -1;
};
struct Region {
std::string name;
int64_t start = 0;
int64_t end = -1;
};
st... |
0fa2b6ebe47b997cd2d8b01ea9a789039dc1ee98bb62f91e194a0158775c2394 | C/C++ | 2,104 | 72 | #pragma once
#include "utils/MoveOnlyFunction.h"
#include "utils/concurrency/task_priority.h"
#include <cstddef>
#include <list>
#include <memory>
#include <queue>
#include <vector>
namespace dorado::utils::concurrency::detail {
using TaskType = utils::MoveOnlyFunction<void()>;
struct WaitingTask {
WaitingTask... |
0d766fe68a0f746b29caa7c6ea1e96c45c5fca50360e1d224c19935a76eb666f | C/C++ | 2,106 | 101 | /**
******************************************************************************
* @file usbd_req.h
* @author MCD Application Team
* @brief Header file for the usbd_req.c file
******************************************************************************
* @attention
*
* Copyright (c) 20... |
42f0a4f3f1c4ecf6f5ebda783db89bd9a03fafff82b37f2c1619cd16b7a4ab29 | C/C++ | 2,107 | 52 | #pragma once
#include <memory>
#include <optional>
#include <string>
#include <string_view>
namespace dorado::alignment {
constexpr inline std::string_view DEFAULT_MM_PRESET{"lr:hq"};
class Minimap2IdxOptHolder;
class Minimap2MapOptHolder;
struct Minimap2IndexOptions {
Minimap2IndexOptions();
std::shared_p... |
31d357b197ad8b65134a79398b388198cb5607024cf3455c6feef9c2e31b1c3e | C/C++ | 2,118 | 66 | #pragma once
#include <string>
#include <string_view>
#include <unordered_map>
#include <unordered_set>
#include <vector>
namespace dorado::barcode_kits {
struct BarcodeKitScoringParams {
int max_barcode_penalty = 9;
int barcode_end_proximity = 75;
int min_barcode_penalty_dist = 3;
int min_separation... |
e31b4c54f55248659f61d66fee60ec05347b066c728f4500ffb1a72e0668e14f | C/C++ | 2,119 | 69 | #pragma once
#include "SpeedEntry.h"
#include <filesystem>
#include <map>
#include <mutex>
#include <span>
#include <string>
#include <vector>
namespace dorado::batchsize_benchmarks {
class BenchmarkCache final {
public:
// Perform an action with the cache lock held.
// Functor will be passed a CacheProxy.
... |
1d6c1bb8943bdf427acbc87d8758a38cde5c2c3a6cc136af971f8300c47cb93d | C/C++ | 2,121 | 100 | #pragma once
#ifdef _WIN32
#include <io.h>
#define NULL_DEVICE "NUL:"
#define Close _close
#define Dup _dup
#define Dup2 _dup2
#define Fileno _fileno
#else
#include <unistd.h>
#define NULL_DEVICE "/dev/null"
#define Close close
#define Dup dup
#define Dup2 dup2
#define Fileno fileno
#endif
#include <stdio.h>
#includ... |
829b102e5bfd11614610f7df9bdc4489d8acc62403164c8a5069fbcc08f4685e | C/C++ | 2,152 | 70 | #pragma once
#include "correct/types.h"
#include "read_pipeline/base/MessageSink.h"
#include <spdlog/spdlog.h>
#include <atomic>
#include <filesystem>
#include <memory>
#include <mutex>
#include <queue>
#include <string>
#include <thread>
#include <unordered_set>
#include <vector>
namespace dorado {
class Correcti... |
69c1640a3585369fe5ccc0fd25925ba0b2d73c0ae1d747a6773aed481306273f | C/C++ | 2,154 | 50 | #pragma once
#include "Minimap2Options.h"
#include <optional>
#include <string>
#include <string_view>
#include <vector>
using namespace std::literals;
namespace argparse {
class ArgumentParser;
}
namespace dorado::alignment::mm2 {
// Retrieves the minimap2 options string from the given args and assigns the remai... |
3410a1d6db242dd3e1c0ae1a58a15de5da064cb47f9a28624534846d8100f563 | C/C++ | 2,193 | 50 | #pragma once
#include <filesystem>
#include <optional>
#include <set>
#include <string>
#include <vector>
namespace dorado::utils {
const std::string TEMP_MODELS_DIR_PREFIX{".temp_dorado_model-"};
std::string get_extension(const std::filesystem::path& path);
std::string get_extension(const std::filesystem::director... |
144fd2e2b0c9f42077a8043e4f3dbaad690133c2c572987d3fea454b441f2921 | C/C++ | 2,238 | 56 | #pragma once
#include "basecall/MetalCaller.h"
namespace dorado::basecall {
namespace model {
struct MetalCRFModelImpl;
} // namespace model
class MetalLSTMCaller final : public MetalCaller {
public:
MetalLSTMCaller(const config::BasecallModelConfig &model_config, float memory_limit_fraction);
~MetalLSTMCa... |
8b1aca4bc212b98105bd89c58403fc10aad72e7c1c9e1f3b84f40d711da3d28e | C/C++ | 2,254 | 76 | #pragma once
#include "DecodedChunk.h"
#include "config/BasecallModelConfig.h"
#include "torch_utils/metal_utils.h"
#include <ATen/core/TensorBody.h>
#include <c10/core/ScalarType.h>
#include <atomic>
#include <condition_variable>
#include <deque>
#include <memory>
#include <mutex>
#include <thread>
#include <vector... |
a8781942df2f2b067c87144d59012b072dbe29c9c230cf05ac17d9b3e147ed47 | C/C++ | 2,277 | 57 | #pragma once
#include <ATen/core/TensorBody.h>
#include <string>
#include <tuple>
#include <utility>
#include <vector>
namespace dorado::utils {
namespace detail {
[[noreturn]] void trim_throw(std::size_t size, const std::pair<int, int>& interval);
} // namespace detail
// Default trim settings.
constexpr float D... |
b674fd010ac8814e9bad26d0799a9729cbb75dccbe39768c9558adb52b83c088 | C/C++ | 2,279 | 62 | #pragma once
#include "torch_utils/gpu_profiling.h"
#include "types.h"
#include <ATen/TensorIndexing.h>
#include <ATen/ops/empty.h>
#include <spdlog/spdlog.h>
#include <filesystem>
#ifdef NDEBUG
#define LOG_TRACE(...)
#else
#define LOG_TRACE(...) spdlog::trace(__VA_ARGS__)
#endif
namespace dorado::correction {
//... |
82aa02335578c4cfa6348998e61570cab82f7a721f49df89a37b16a6c19df52c | C/C++ | 2,307 | 66 | #pragma once
#include "adapter_info.h"
#include "hts_utils/hts_types.h"
#include "utils/types.h"
#include <mutex>
#include <string>
#include <vector>
namespace dorado {
namespace adapter_primer_kits {
class AdapterPrimerManager;
struct Candidate {
std::string name;
std::string front_sequence;
std::stri... |
3808ce741d1ce83cd9f8bab616d873c91fd7d1fde6ef952bc35fe4612a76ad64 | C/C++ | 2,315 | 69 | #pragma once
#include "utils/AsyncQueue.h"
#include "utils/concurrency/Task.h"
#include "utils/hardware_interference_size.h"
#include <atomic>
namespace dorado::utils::concurrency {
// A pool of tasks that the workers will pull work from.
//
// The pool consists of |num_queues| queues, each of size |q_capacity|.
cl... |
4a5fab82ee97cfddf64056208a861e53a6fb1f59f8199e4dfc0829fd7e1c7055 | C/C++ | 2,336 | 102 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : usb_device.h
* @version : v1.0_Cube
* @brief : Header for usb_device.c file.
******************************************************************************
... |
85365d22cdd45f2997e1747d2ecb59bd2bfc09e2accf43b7f4e17737c8c649ae | C/C++ | 2,348 | 89 | #pragma once
// Backport of std::function_ref.
#include <functional>
#include <new>
#include <type_traits>
#include <utility>
namespace dorado::utils {
namespace detail {
template <bool IsConst, typename R, typename... Args>
class FunctionRefBase {
using FunctionPtr = R (*)(Args...);
// |m_invoke| is set ... |
0fec79457e010044dae6ebb76e709ad270a6e66b8f4f59dea1adc32c5cdba833 | C/C++ | 2,363 | 74 | #pragma once
#include "secondary/common/bam_file.h"
#include "secondary/consensus/sample.h"
#include "secondary/features/encoder_base.h"
#include <ATen/ATen.h>
#include <cstdint>
#include <mutex>
#include <string>
#include <vector>
namespace dorado::secondary {
struct CountsResult {
at::Tensor counts;
std:... |
7ce73b57c77bb433f6e0e4126096257ed3cc99315f272ed59a794789811ee65c | C/C++ | 2,373 | 86 | #pragma once
#include "string_utils.h"
namespace dorado::utils {
/**
* Stream-like object that splits elements on @a Separator.
* Note that trailing elements are ignored.
*/
template <char Separator>
class SeparatedStream {
std::string_view m_data;
bool m_eof = false;
template <typename T>
static... |
528f06a57024d91b8cac119459b5de5a74889cb42bffbb6eed52676897ce8b69 | C/C++ | 2,384 | 62 | /****************************************************************************
**
** Copyright (c) 2008-2018 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullError.h#4 $$Change: 2549 $
** $DateTime: 2018/12/28 22:24:20 $$Author: bbarber $
**
***********************************************... |
c230899c6f73aa899267578f9fa5c019655315916481f8e57dc961a3b0f38092 | C/C++ | 2,403 | 73 | #pragma once
// TSan's init breaks the call to __cpu_indicator_init (which determines which implementation to take)
#if defined(__GNUC__) && defined(__x86_64__) && !defined(__clang__) && !defined(__SANITIZE_THREAD__)
#define ENABLE_AVX2_IMPL 1
#include <immintrin.h>
#else
#define ENABLE_AVX2_IMPL 0
#endif
#if defined... |
fc7ffbed8ff7752453bb510493b43165ef29f4c5091e50fb6d0c4c8652d4f560 | C/C++ | 2,422 | 113 | /**
******************************************************************************
* @file usbd_ioreq.h
* @author MCD Application Team
* @brief Header file for the usbd_ioreq.c file
******************************************************************************
* @attention
*
* Copyright (c... |
3c21dfc5dda858c7b1968610e185f1822d33fe2e31f46a5a8dbc43d9e37f82e3 | C/C++ | 2,441 | 60 | #pragma once
#include "read_pipeline/base/ReadPipeline.h"
#include "utils/types.h"
#include <cstdint>
#include <map>
#include <memory>
#include <string>
#include <variant>
#include <vector>
namespace dorado {
namespace basecall {
class ModelRunnerBase;
using RunnerPtr = std::unique_ptr<ModelRunnerBase>;
} // names... |
e07411a427e650242104956a92eba68e4c0c407547d20d0526268d2acba3a177 | C/C++ | 2,484 | 66 | #pragma once
#include "data_loader/DataLoader.h"
#include "read_pipeline/base/ReadPipeline.h"
#include <memory>
#include <vector>
class MessageSinkToVector : public dorado::MessageSink {
public:
MessageSinkToVector(size_t max_messages, std::vector<dorado::Message>& messages)
: MessageSink(max_message... |
42ffa0bbcec626f25cbaafd04f16c1f0628598aa08e7649b36b444c4fe6af5ff | C/C++ | 2,511 | 70 | #pragma once
#include "Minimap2IndexSupportTypes.h"
#include "Minimap2Options.h"
#include "hts_utils/header_sq_record.h"
#include <minimap.h>
#include <memory>
#include <optional>
#include <string>
#include <utility>
#include <vector>
namespace dorado::alignment {
struct IndexReaderDeleter {
void operator()(mm... |
76612dafb17072fda18273e325ae290297830db83124991f8f17bd07f7f73a8e | C/C++ | 2,558 | 76 | #pragma once
#include "utils/stats.h"
#include <ATen/core/TensorBody.h>
#if DORADO_CUDA_BUILD
#include <c10/cuda/CUDAStream.h>
#endif
#include <atomic>
#include <string>
#include <vector>
namespace dorado::config {
struct ModBaseModelConfig;
}
namespace dorado::modbase {
class ModBaseCaller;
class ModBaseRunner {... |
9d85caed061945147c877efab2e3685064815849dd317d7918d66732b833053c | C/C++ | 2,577 | 61 | /**
******************************************************************************
* @file usbd_desc_template.h
* @author MCD Application Team
* @brief Header for usbd_desc_template.c module
******************************************************************************
* @attention
*
* Cop... |
17f724f8c73f6910607ea04360a9f6ee782bb2397cb8165fddfa2203e3475e88 | C/C++ | 2,619 | 119 | #ifndef SCALAR_SSE_H
#define SCALAR_SSE_H
#include <assert.h>
#include <stdint.h>
#include <string.h>
typedef union m128i {
uint8_t u8[16];
int16_t i16[8];
} __m128i;
static inline __m128i _mm_set1_epi32(int32_t n) {
assert(n >= 0 && n <= 255);
__m128i r; memset(&r, n, sizeof r); return r;
}
static inline __m12... |
c847b6e640ba3e4dfd8d89e4dcbcd6f17b50fa013343b39d2a7bd6c607841a4b | C/C++ | 2,640 | 131 | #ifndef KSTRING_H
#define KSTRING_H
#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
#ifndef KSTRING_T
#define KSTR... |
e3d9afe7ddbbf3ca34a8591585f8dbba7b5afb94cc14257313faad8c41ee0a89 | C/C++ | 2,644 | 54 | #pragma once
#include <ATen/ATen.h>
#include <cstdint>
#include <string>
#include <tuple>
#include <vector>
namespace dorado::secondary {
std::tuple<at::Tensor, std::vector<std::string>> reorder_chunk(
const at::Tensor& chunk,
const std::vector<std::string>& prev_rids_out,
const std::vector<... |
0b8b5831c7d5c0ec4fa679371a6ee28511ec1be5009c3d7346ef0168a46397a4 | C/C++ | 2,651 | 69 | #pragma once
#include "alignment/BedFileAccess.h"
#include "alignment/IndexFileAccess.h"
#include "alignment/Minimap2Options.h"
#include "hts_utils/header_sq_record.h"
#include "read_pipeline/base/ClientInfo.h"
#include "read_pipeline/base/MessageSink.h"
#include "utils/concurrency/AsyncExecutor.h"
#include <memory>
... |
a6be4e284ffc49e20ad2de8198c7ccbed79c00b570b1f7b7583efd0b01b4ae75 | C/C++ | 2,672 | 78 | #pragma once
#include "utils/parameters.h"
#include <filesystem>
#include <optional>
#include <string>
namespace dorado::config {
// Stores basecaller parameters and manages the overwrite priority from various setters
// where Default < Config < CLI Argument < Forced.
class BatchParams {
public:
// Overwrite pr... |
4daca69dcca06289f6108340714f19f9f9dbe4a54b36c72eecf9dbe999395bb2 | C/C++ | 2,782 | 68 | #pragma once
#include <ATen/core/TensorBody.h>
#include <cstddef>
#include <filesystem>
#include <iosfwd>
#include <string>
#include <vector>
namespace dorado::utils {
// Serialise Torch tensor to disk.
void serialise_tensor(const at::Tensor& t, const std::string& path);
// Load serialised tensor from disk.
std::ve... |
fad7764eecd0a7b024e083d3d704549e027f86bbf67a5acf8e67fe16d0c991ec | C/C++ | 2,784 | 107 | #pragma once
#include "kits.h"
#include <iosfwd>
#include <set>
namespace dorado::models {
/*
Enumerate the options available for auto model selection.
`UNRECOGNISED` is used to default back to a path
*/
enum class ModelVariant : uint16_t {
AUTO,
FAST,
HAC,
SUP,
NONE // NONE must be last
};
/... |
7bb9ea3b89406c4afb9ce3ce60ccc2f3c0c6bef20bae8416343beef5a0d0d783 | C/C++ | 2,792 | 93 | #pragma once
#include <cstdint>
#include <memory>
#include <variant>
namespace dorado {
class ClientInfo;
class DuplexRead;
class HtsData;
class ReadCommon;
class SimplexRead;
struct CorrectionAlignments;
struct ReadPair;
using CorrectionAlignmentsPtr = std::unique_ptr<CorrectionAlignments>;
using DuplexReadPtr = s... |
f4d2f9f9d071cb5a01562181a81c8d4da3ddfbde435486bee880d8f7b83aac3c | C/C++ | 2,805 | 69 | #pragma once
#include <ATen/Tensor.h>
#include <filesystem>
#include <iosfwd>
#include <vector>
namespace dorado::correction {
// clang-format off
struct OverlapWindow {
// CorrectionAlignments overlap vector index
int overlap_idx = -1;
int win_tstart = -1; // Window target start position.
... |
5f0de5db377ad373d4c844a3cbd45224844635e383e2ca9b5bc96f32ee2985d7 | C/C++ | 2,819 | 131 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : usbd_cdc_if.h
* @version : v1.0_Cube
* @brief : Header for usbd_cdc_if.c file.
*****************************************************************************... |
47d49ae7b6a5318a5100ece61d0e220f11a5c373add8fdf09b5e3995cc747721 | C/C++ | 2,838 | 101 | #pragma once
#include "config/ModBaseModelConfig.h"
#include "modbase/MotifMatcher.h"
#include "torch_utils/module_utils.h"
#include "utils/stats.h"
#if DORADO_CUDA_BUILD
#include <c10/cuda/CUDAStream.h>
#endif
#include <torch/nn.h>
#include <atomic>
#include <condition_variable>
#include <deque>
#include <filesystem... |
ac1eee56a3a79bf601060461329dab3615ccb9caad7a1cb577c81d038fca2896 | C/C++ | 2,842 | 92 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
23106f81a993f61420c7858bea7a30440e66b55bd278cceb2a79880e791cb627 | C/C++ | 2,846 | 87 | #pragma once
#include "hts_utils/HeaderMapper.h"
#include "hts_utils/hts_file.h"
#include "interface.h"
#include <memory>
#include <string>
namespace dorado {
class HtsData;
namespace hts_writer {
using OutputMode = utils::HtsFile::OutputMode;
struct HtsFileWriterConfig {
OutputMode mode;
int threads;
... |
4542baf8ffe78bfe442714756af696ce0b01ab746a6d7f59d528f60f9b1df24d | C/C++ | 2,872 | 91 | #pragma once
#include <ATen/Tensor.h>
#include <torch/nn/module.h>
#include <torch/nn/modules/activation.h>
#include <torch/nn/modules/batchnorm.h>
#include <torch/nn/modules/container/modulelist.h>
#include <torch/nn/modules/container/sequential.h>
#include <torch/nn/modules/conv.h>
#include <torch/nn/modules/dropout... |
fee9de3e6a2fcda5ad382a00714f2f6365934b5a2ad538a8188c58826c1ca76e | C/C++ | 2,874 | 64 | #pragma once
#include "sample.h"
#include "secondary/common/region.h"
#include <cstdint>
#include <iosfwd>
#include <optional>
#include <vector>
namespace dorado::secondary {
struct TrimInfo {
int64_t start = 0;
int64_t end = -1;
bool heuristic = false;
};
/**
* \brief Checks the start/end coordinates... |
bf3213aee2ffb202df135fe82218426084138bac593b1f174cb437a58a779f7c | C/C++ | 2,900 | 94 | #pragma once
#include "CorrectionAligner.h"
#include "aligner/Minimap2Aligner.h"
#include "alignment/Minimap2Index.h"
#include "read_pipeline/base/messages/CorrectionAlignments.h" // GCC 11's unordered_map needs this
#include "utils/AsyncQueue.h"
#include "utils/stats.h"
#include <atomic>
#include <condition_variabl... |
83e947a1ce86e4208d56f2f43174f213d2a6147d25728d21d427cb6d2998f6e5 | C/C++ | 2,906 | 68 | #pragma once
#include "demux/AdapterDetector.h"
#include "demux/adapter_info.h"
#include <string>
#include <unordered_map>
#include <vector>
namespace dorado::adapter_primer_kits {
class AdapterPrimerManager {
public:
/** Default Constructor.
* This provides a manager that uses the above hard-coded adapte... |
7ab22e862455ff23db3bc51e55b42d9e1c4154b138d124151bfc77b2d2d2fefa | C/C++ | 2,930 | 66 | #pragma once
#include <ATen/ATen.h>
#include <torch/nn/module.h>
#include <optional>
namespace dorado::secondary {
/**
* \brief Attention helper which dispatches to FlashAttention3 when available and falls back to
* PyTorch SDPA otherwise.
*/
class FlashAttentionModuleImpl : public torch::nn::Module {
pub... |
2de8f782e72568fb58521bd7abcfb8da89697ee3d95dcd6ce908c88800b34ee4 | C/C++ | 2,938 | 94 | #pragma once
#include "SimpleProgressBar.h"
#include "utils/stats.h"
#include <chrono>
#include <cstdint>
#include <map>
#include <string>
namespace dorado {
// Collect and calculate throughput related
// statistics for the pipeline to track dorado
// overall performance.
class ProgressTracker {
public:
enum Mo... |
2cff5fdf95ac9bca216a1cfea00f74b5c84f3faa19878974485873074cac37af | C/C++ | 2,940 | 94 | /* The MIT License
Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation ... |
d8fa7735942ce49c45be89e732f07bd36c70b75dbeff6ee1877b07741544491c | C/C++ | 2,977 | 143 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : usbd_desc.c
* @version : v1.0_Cube
* @brief : Header for usbd_conf.c file.
******************************************************************************
... |
cb4bf84d0e09361c150fc2f74e470919cd206ec710d421dc79ab50f6b4b3070e | C/C++ | 2,997 | 67 | #pragma once
#include <ATen/core/TensorBody.h>
#include <cstdint>
#include <string>
#include <utility>
#include <vector>
namespace dorado::modbase {
/// Calculates new scaling values for improved modified base detection
class ModBaseScaler {
private:
const std::vector<float>& m_kmer_levels;
const size_t m_k... |
520ef4eeba44a2caaafcd38b8fe9237d021a4dde03b95fdef0927a475d748615 | C/C++ | 3,077 | 103 | #pragma once
#include <array>
#include <cstdint>
#include <iosfwd>
#include <string>
#include <tuple>
#include <vector>
namespace dorado {
// clang-format off
// Enum for handling CIGAR ops
enum class CigarOpType : uint8_t {
M = 0, // Alignment match. Can be either = or X.
I = 1, // Inserti... |
4db5f99eb0ad1638bc1e725bc23c5a144d89981c9f17ca3b54a2662b2eeeb497 | C/C++ | 3,087 | 86 | #pragma once
#include "config/BasecallModelConfig.h"
#include "torch_utils/metal_utils.h"
#include <torch/nn.h>
#include <vector>
namespace dorado::nn::metal {
struct MetalLinearImpl : torch::nn::Module {
MetalLinearImpl(int insize, int outsize, bool has_bias);
};
TORCH_MODULE(MetalLinear);
struct MetalConv1... |
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