sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f83f771993104ad704226de00cb3a6c5cf816fd41b4cfb3e485a8f5b2e8489e9 | C++ | 3,715 | 105 | #include "DBWriter.h"
#include "Debug.h"
#include "DBReader.h"
#include "Util.h"
#include "Matcher.h"
#include "FileUtil.h"
#ifdef OPENMP
#include <omp.h>
#endif
int extractalignedregion(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(arg... |
2825bd75dfbfd69c4406d6c0b8bbaf10ab432f88fed71be6accdf7c33a0509de | C++ | 3,734 | 90 | #include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "TaxonomyExpression.h"
#include "MappingReader.h"
#ifdef OPENMP
#include <omp.h>
#endif
int filtertaxseqdb(int argc, const char **argv, const Command& command) {
Parameters& ... |
8fed1e0ebdc7ef4cb4a49358d25062b4afae774e04b10070536b5accd86c5d42 | C++ | 3,776 | 144 | /**
* Copyright 2015-2025, XGBoost Contributors
*/
#include "cuda_rt_utils.h"
#if defined(XGBOOST_USE_CUDA)
#include <cuda_runtime_api.h>
#include <algorithm> // for max
#endif // defined(XGBOOST_USE_CUDA)
#include <cstddef> // for size_t
#include <cstdint> // for int32_t
#include <mutex> // f... |
85aca22df08da1ede4054fc5079cebd4d48b198f899864155917f19a04eea7bb | C++ | 3,778 | 169 | #include <boost/date_time/posix_time/posix_time.hpp>
#include "caffe/common.hpp"
#include "caffe/util/benchmark.hpp"
namespace caffe {
Timer::Timer()
: initted_(false),
running_(false),
has_run_at_least_once_(false) {
Init();
}
Timer::~Timer() {
if (Caffe::mode() == Caffe::GPU) {
#ifndef CPU_ONL... |
44062e0a21bfff4607d8c5421534e425bc731d6e0823bb850837a7048d422e16 | C++ | 3,796 | 106 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "kraken2_headers.h"
#include "mmap_file.h"
#include "utilities.h"
using namespace kraken2;
using std::string;
using std::unordered_map;
using std::vector;
int main... |
de4483608134981925a164b446a57cbcf6075c05610693b2c2fca5135db2b5db | C++ | 3,819 | 90 | #include <cassert>
#include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
namespace linclust {
#include "easycluster.sh.h"
}
void setEasyLinclustDefaults(Parameters *p) {
p->spacedKmer = false;
p->removeTmpFiles = true;
p->covThr = 0.8;
p->evalTh... |
0a7f0dbc59f221e952361f9245a5e0030bad95f68b6a9f5ecc587195535b4cf2 | C++ | 3,831 | 133 | /**
* Copyright 2019-2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <fstream>
#include <memory>
#include <vector>
#include "../filesystem.h" // dmlc::TemporaryDirectory
#include "../helpers.h"
#include "xgboost/data.h"
namespace xgboost {
TEST(SparsePage, PushCSC) {
std::vector<bst_idx_t> off... |
39b128e13afb765f20c67d6b6fa21cf65832cc736c0721f52cb0c0b7647cd217 | C++ | 3,870 | 186 | #include "caffe/common.hpp"
#include "caffe/syncedmem.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
SyncedMemory::SyncedMemory()
: cpu_ptr_(NULL), gpu_ptr_(NULL), size_(0), head_(UNINITIALIZED),
own_cpu_data_(false), cpu_malloc_use_cuda_(false), own_gpu_data_(false) {
#ifndef CPU_ONLY
#ifdef DE... |
e9abe5e979ea34bc0e8fd9a0a7fa0c0f0b127525d230ec6588a1b683825bf058 | C++ | 3,882 | 101 | /**
* Copyright 2018-2023 by XGBoost Contributors
* \author Tianqi Chen, Rory Mitchell
*/
#include <xgboost/linear_updater.h>
#include "coordinate_common.h"
namespace xgboost::linear {
DMLC_REGISTRY_FILE_TAG(updater_shotgun);
class ShotgunUpdater : public LinearUpdater {
public:
// set training parameter
vo... |
49ea7a71525edf0db012d321a6c9ec14dd8fb261b0cd6820f7fd678accbe0004 | C++ | 3,925 | 104 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "aa_translate.h"
#include <cstdint>
using std::string;
using std::vector;
namespace kraken2 {
/*
This *was* the map, which was ridiculously slow. Note that order... |
8ac1604d3fa30baccebd46b6900dd9fb4dd65d46624554d47eeca757601157d7 | C++ | 3,925 | 107 | #include <functional>
#include <utility>
#include <vector>
#include "caffe/layers/accuracy_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void AccuracyLayer<Dtype>::LayerSetUp(
const vector<Blob<Dtype>*>& bottom, const vector<Blob<Dtype>*>& top) {
top_k_ = this->l... |
2f984ff44ff1219913bee61d905c588aa4f19d756786ec13c32033c7fdc1ee8d | C++ | 3,926 | 109 | // Copyright 2005, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
3dcb71df76b4df689a1e63419baa31a7d6aedaf6e21e3004766a4bbcb1a73861 | C++ | 3,928 | 112 | #include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "simd.h"
#include "KSeqWrapper.h"
#include "MsaFilter.h"
#include "MultipleAlignment.h"
MultipleAlignment::MSAResult readMSA(const std::string &a3mPath, const SubstitutionMatrix &subMat) {
KSeqWrapper* kseq = KSeqFactory(a3mPath.c_str());
Mult... |
901c0dc4ea0e414d6a3e5e257bbdd38ed94147f7c98624ed09bd35ecfa109c97 | C++ | 3,934 | 117 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
35491f51406d8fd10a211dc74a7be40031dedaadda970121e91acb02473e7c55 | C++ | 3,940 | 101 | #include "Parameters.h"
#include "Util.h"
#include "PrefilteringIndexReader.h"
#include "MemoryMapped.h"
#include "IndexReader.h"
#include "SubstitutionMatrix.h"
#include "NucleotideMatrix.h"
// #define HAVE_CUDA 1
#ifdef HAVE_CUDA
#include "GpuUtil.h"
#endif
#include <random>
#include <fcntl.h>
#include <sys/mman.h>... |
ab4f01629441758c2b1595e27bc391b4b3821d8cdf9323217ae83d0342b35a38 | C++ | 3,946 | 127 | #include "confidence_cut.h"
#ifdef _OPENMP
#include <omp.h>
#endif
#include <Rcpp.h>
#include <algorithm> // std::sort
#include <set>
#include "get_information.h"
#include "environment.h"
namespace miic {
namespace reconstruction {
using std::string;
using std::vector;
using namespace miic::computation;
using nam... |
bf3175f534e45e565e7a0b3b9aeaf974b0a72d1a83c280a150a01fbc6577f402 | C++ | 3,960 | 118 | // Copyright 2008 Google Inc.
// All Rights Reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions a... |
61b163c7e5a0fc88b50cb519b0865c4c8a7c018d6cc67afddebc00c05b32043c | C++ | 3,974 | 119 | #include <Rcpp.h>
#include <algorithm> // std::max_element
#include <array>
#include <numeric> // std::iota
#include "get_information.h"
#include "environment.h"
#include "linear_allocator.h"
#include "r_cpp_interface.h"
#include "utilities.h"
constexpr int kStepMax = 50;
using Rcpp::_;
using Rcpp::as;
using Rcpp... |
2fb550a2e6ac41e34f0795c2bcce0917f7e6657cf1a46da8eaa6e024490635f9 | C++ | 3,976 | 144 | /*++
Module Name:
ParallelTask.cpp
Abstract:
Parallel task management
Environment:
User mode service.
--*/
#include "stdafx.h"
#include "ParallelTask.h"
#include "Error.h"
using std::max;
ParallelCoworker::ParallelCoworker(int i_numThreads, bool i_bindToProcessors, ParallelWorkerManager* i_manager... |
1ae526d9a5bc39bf1bcd5fc78942da420034624d3f5712602085135454887c6a | C++ | 3,981 | 103 | /**
* Copyright 2018-2025, XGBoost Contributors
* \author Rory Mitchell
*/
#include <xgboost/linear_updater.h>
#include "./param.h"
#include "../common/timer.h"
#include "coordinate_common.h"
#include "xgboost/json.h"
namespace xgboost::linear {
DMLC_REGISTER_PARAMETER(CoordinateParam);
DMLC_REGISTRY_FILE_TAG(upd... |
e9234f7d9a42ac15bb8220813eef6d82d5edaf5601ed2d94e9791e1e3f5b4dc7 | C++ | 3,982 | 108 | #include "RayEnvManager.h"
RayEnvManager::
RayEnvManager(std::string meta_file)
{
dart::math::seedRand();
mEnv = new MASS::Environment(false);
if (!mEnv->Initialize_from_path(std::string(meta_file)))
mEnv->Initialize_from_text(meta_file);
}
void RayEnvManager::
SetParamState(py::array_t<flo... |
9e48868a6aa389a44525f9da4b59dd538092128db766bba1a9ca53212bffeddb | C++ | 3,992 | 124 | #ifdef USE_HDF5
#include <string>
#include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/layers/hdf5_output_layer.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caffe/util/hdf5.hpp"
#include "caffe/util/io.hpp"
#include "caffe/test/test_caffe_main.hpp"
nam... |
716746047818c4e23243615427da60e1095af6c659709735c6e5695e1d78e64e | C++ | 4,015 | 101 | #include "Parameters.h"
#include "FileUtil.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include <climits>
int createsubdb(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0... |
753d340b18ae234045fe9f324bbd9e29d0397c2875fd4870cd13425c36a32be4 | C++ | 4,016 | 92 | #include "Debug.h"
#include "Util.h"
#include "Parameters.h"
#include "FileUtil.h"
#include "CommandCaller.h"
#include <cassert>
#include "update_clustering.sh.h"
extern void setClusterAutomagicParameters(Parameters& par);
void setClusterUpdateDefaults(Parameters *p) {
p->alignmentMode = Parameters::ALIGNMENT_M... |
9e2d37b0b14a627859d94fb090aa6433cf66e6bcb70d34d9ae46ab94cda6d450 | C++ | 4,052 | 114 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
2992c8b55459bd708d0adcdee04844e5869bb857bceb2bfa99e02041259e722a | C++ | 4,055 | 148 | #include "BacktraceTranslator.h"
const char* binary_name = "test_backtracetranslator";
int main(int, const char**) {
// s1 5 ATT-GCA 11
// s2 3 ATTTG-- 8
// s3 6 --T-G-A 9
// AB, BC
// ATTTG-- MMMIM
// ATT-GCA
// ATTGCA MMMIM
// --TG-A MMIM
// s2 -> s1, s1-> s3 => infer s2 -> s1 ... |
21ee1cb86da5a0b4ac5e7014e3476edb9f5bd518d908825089afc9e985f9291c | C++ | 4,066 | 165 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
0bd5962f32ebb9e76f4e458a15978e4b94c2ec0bc4d4bdc0e0c71f79a8a6f3ae | C++ | 4,080 | 124 | #include "Parameters.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "GzReader.h"
#include <algorithm>
#include <map>
int convertmsa(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);... |
32eb65666293f8d9207df63e7d207c5e6c8488929516c9d512a5c86c365ae4bc | C++ | 4,080 | 124 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <unistd.h>
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <vector>
#include <iostream>
#include <sys/types.h>
#include <sys/stat.h>
#include "... |
227fba57ad3438c28951d869e45710c6cc55986b873b1f1c9603cb8bccf226fd | C++ | 4,082 | 122 | /**
* Copyright 2023-2024, XGBoost contributors
*
* Some other tests for federated learning are in the main test suite (test_learner.cc).
*/
#include <dmlc/parameter.h>
#include <gtest/gtest.h>
#include <xgboost/data.h>
#include <xgboost/objective.h>
#include "../../../../src/collective/communicator-inl.h"
#includ... |
76754de670c942d0d820b621eb9fd5a77e720749e0577f99ac3c5cf0c35fb33b | C++ | 4,102 | 114 | /*
* Copyright (C) 2019-2026 Matthias Klumpp <matthias@tenstral.net>
*
* Licensed under the GNU Lesser General Public License Version 3
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Founda... |
a98ebfb35fe528a775fcc643f0cf56af5a748dca5038f6e37682b63a3fa40ad7 | C++ | 4,114 | 130 | #include <algorithm>
#include <cmath>
#include <vector>
#include "caffe/layer.hpp"
#include "caffe/layers/lstm_layer.hpp"
namespace caffe {
template <typename Dtype>
inline Dtype sigmoid(Dtype x) {
return 1. / (1. + exp(-x));
}
template <typename Dtype>
inline Dtype tanh(Dtype x) {
return 2. * sigmoid(2. * x) -... |
48acee01493fdac9180e0228063404c02bcb417db430ed699389b887fc8b0c51 | C++ | 4,118 | 136 | #include <boost/thread.hpp>
#include <vector>
#include "caffe/blob.hpp"
#include "caffe/data_transformer.hpp"
#include "caffe/internal_thread.hpp"
#include "caffe/layer.hpp"
#include "caffe/layers/base_data_layer.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caffe/util/blocking_queue.hpp"
namespace caffe {
templa... |
02f908af476b288565adaeaea3c8a3a0d04bd3c082dd3bb6e1f258a800131af4 | C++ | 4,125 | 154 | // Copyright 2003, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
0883fb76d83e50b17a53eca56d6de7e65fcc1d3981fcb736e129b9f5d0327c09 | C++ | 4,163 | 110 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
e2ad56228aa77680eaf0b682d858fc210e6ffb115bbaaa31e95a26ca113f782e | C++ | 4,183 | 139 | /*++
Module Name:
HitDepth.cpp
Abstract:
Special function to find the seed with the minimum hit depth to align each
locus in a set of contigs.
Authors:
Bill Bolosky, March, 2022
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "Compat.h"
#include "Histog... |
d8a7d16c183153ac0284e8fb704a9e46f32f3e6c7b6d4fb857f4b27216682826 | C++ | 4,185 | 108 | #include <cstdio>
#include <Parameters.h>
#include "DBReader.h"
#include "Debug.h"
#include "Util.h"
int result2flat(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
DBReader<DBKeyType> querydb_heade... |
9a59dcc31de5e09ef84a929062c0e0650f827000ef68a1b81552cb611eb3d1dd | C++ | 4,188 | 85 | #include "stdafx.h"
#include "TestLib.h"
#include "AffineGapVectorized.h"
#include "LandauVishkin.h"
// Test fixture for all the affine gap tests
struct AffineGapVectorizedTest {
AffineGapVectorized<> ag;
AffineGapVectorizedTest() : ag(1, 4, 6, 1, 10, 5) {
initializeLVProbabilitiesToPhredPlus33();
... |
2f60304f9f6badeb72764f210b6a665b41d3d2b5bdfe9115bf901b358db3e9ce | C++ | 4,194 | 137 | #include "stdafx.h"
#include "TestLib.h"
#include "LandauVishkin.h"
struct EventTest;
struct TestContext {
EventTest* parent;
int index;
SingleWaiterObject singleWaiterObject;
void init(EventTest* parent, int i);
};
struct EventTest {
EventObject event;
TestContext* contexts;
bool bind;
volatile int... |
5e62737870c2f3623881f67dee00a92e7a43bff0801f8092b566f6007694853b | C++ | 4,206 | 118 | /*
* convert2fasta
* written by Milot Mirdita <milot@mirdita.de>
*/
#include <cstring>
#include <cstdio>
#include <string>
#include <vector>
#include "Parameters.h"
#include "DBReader.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
const char hea... |
458c49ad1dfe891cdd817423056defa9dbf853cb4c185cb6731d9f8c37605585 | C++ | 4,215 | 137 | // a sketch of what the new API might look like
#include "yaml-cpp/yaml.h"
#include <iostream>
int main() {
{
// test.yaml
// - foo
// - primes: [2, 3, 5, 7, 11]
// odds: [1, 3, 5, 7, 9, 11]
// - [x, y]
// move-like semantics
YAML::Value root = YAML::Parse("test.yaml");
std::cout... |
894b64c1484ce01a389ff71e50a830808ccbecf2dc6995e82c17b345a6bf4200 | C++ | 4,216 | 112 | #include "Parameters.h"
#include "Util.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Matcher.h"
#ifdef OPENMP
#include <omp.h>
#endif
int summarizeresult(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, ... |
bdc6c2ada9822769f2d453a2f749dc00e74475bfc1cb4f9fc36d7d542be08ceb | C++ | 4,220 | 164 | /*!
* Copyright 2017-2019 XGBoost contributors
*/
#include <gtest/gtest.h>
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wtautological-constant-compare"
#pragma GCC diagnostic ignored "-W#pragma-messages"
#include <xgboost/objective.h>
#pragma GCC diagnostic pop
#include <xgboost/context.h>
#include "... |
55d1d7c26dcafb122065d97c0dd205189d4474db48942b348f704bca91e54804 | C++ | 4,223 | 146 | //
// Created by mad on 10/26/15.
//
#include <iostream>
#include <queue>
#include "SubstitutionMatrix.h"
#include "Sequence.h"
const char* binary_name = "test_kwaymerge";
struct KmerEntry{
unsigned int seqId;
short diagonal;
KmerEntry(){};
KmerEntry(unsigned int seqId, short diagonal) : seqId(seqId... |
10520cf72773611b2f325a264fae622fb944528b54b7fb13b151b4bdb9e0e09b | C++ | 4,235 | 181 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your opt... |
d6018bf1ac28e5541332dd07f865e27b4f9cd09b973d9a9a7ffe079851ece421 | C++ | 4,236 | 174 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* colon.cpp
*
* Code generation for function 'colon'
*
*/
/* Include files */
#include "colon.h"
#include "m... |
8647933d6276c96ff27e5beaf3ba1bede63e61e9cec92ec3139a40403ae38f85 | C++ | 4,297 | 152 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* sum.cpp
*
* Code generation for function 'sum'
*
*/
/* Include files */
#include "sum.h"
#include "eml_int... |
95b1e548f8cb86e9e894fe4cf96981bf6df4c61c6a3aa73b507ee34296792706 | C++ | 4,298 | 127 | // Copyright 2013, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
bada8c327e434b4406840fafdd19ec521818717e018744a0ac8f772815ef9394 | C++ | 4,313 | 153 | /**
* Copyright 2022-2024, XGBoost Contributors
*/
#include "threading_utils.h"
#include <algorithm> // for max, min
#include <exception> // for exception
#include <filesystem> // for path, exists
#include <fstream> // for ifstream
#include <string> // for string
#include "common.h" // for DivRoundUp... |
bc7e898d39bcd85345c3192f273ab6ccb4c8691168ca46c8cdc71fe9cc46744c | C++ | 4,313 | 136 | #ifdef USE_OPENCV
#include <opencv2/core/core.hpp>
#endif // USE_OPENCV
#include <stdint.h>
#include <vector>
#include "caffe/data_transformer.hpp"
#include "caffe/layers/data_layer.hpp"
#include "caffe/util/benchmark.hpp"
namespace caffe {
template <typename Dtype>
DataLayer<Dtype>::DataLayer(const LayerParameter... |
e97163b999f88875e700acdad1f86a8cbe5d946eec1ab676bc5dffe1cb5225ee | C++ | 4,322 | 105 | #include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
int createseqfiledb(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
DBReader<DB... |
38a267431be7bdb39e70963bd2ecbb1559532c538c050ce73766199a52edff95 | C++ | 4,356 | 116 | #include "Matcher.h"
#include "DBReader.h"
#include "Debug.h"
#include "DBWriter.h"
#include "Util.h"
#include "Parameters.h"
#include <map>
#ifdef OPENMP
#include <omp.h>
#endif
int subtractdbs(int argc, const char **argv, const Command& command) {
Parameters &par = Parameters::getInstance();
par.parseParam... |
ac35cdf5c9d11933fa9a8f3c9f479dd7350d2d4386595a7d782bc4414a9792e3 | C++ | 4,368 | 129 | //
// This script converts the MNIST dataset to the leveldb format used
// by caffe to train siamese network.
// Usage:
// convert_mnist_data input_image_file input_label_file output_db_file
// The MNIST dataset could be downloaded at
// http://yann.lecun.com/exdb/mnist/
#include <fstream> // NOLINT(readability/... |
4bd4db5d78370d87cc00e75f2a67dc1d4ace1df309a766b2380989d41cccfbc3 | C++ | 4,399 | 163 | /**
* Copyright 2018-2024, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h>
#include <xgboost/objective.h>
#include "../../../src/objective/adaptive.h"
#include "../../../src/tree/param.h" // for TrainParam
#include "../helpers.h"
#include "test_regression_obj.h"
namespace xgboost {
TE... |
7f8c4e5541211f852bb31b750172ca6333718207e868f074cafbdeb097c010c2 | C++ | 4,414 | 121 | #ifdef HAVE_CUDA
#include "GpuUtil.h"
#include "Debug.h"
#include "FileUtil.h"
#include "PrefilteringIndexReader.h"
#include <cstring>
#include <fcntl.h>
#include <iostream>
#include <sys/mman.h>
#include <unistd.h>
#include <utility>
#include <thread>
extern const char* version;
std::string GPUSharedMemory::getShm... |
c6314e899ac62d1ec7866f9f862bf305912e6eff8ce15e5b96babed14aa66d76 | C++ | 4,422 | 124 | #include "my_application.h"
#include <flutter_linux/flutter_linux.h>
#ifdef GDK_WINDOWING_X11
#include <gdk/gdkx.h>
#endif
#include "flutter/generated_plugin_registrant.h"
struct _MyApplication {
GtkApplication parent_instance;
char** dart_entrypoint_arguments;
};
G_DEFINE_TYPE(MyApplication, my_application, GT... |
1f0579e8c04b62739b09ac530e4344b220a930156a330b25dd9cd21fe777ac27 | C++ | 4,474 | 166 | extern "C" {
#include <linux/errno.h>
#include <linux/xxhash.h>
}
#include <gtest/gtest.h>
#include <array>
#include <iostream>
#include <memory>
#include <string>
#define XXH_STATIC_LINKING_ONLY
#include <xxhash.h>
using namespace std;
namespace {
const std::array<std::string, 11> kTestInputs = {
"",
"0",
"012... |
43e0819eb98d1adb984b47ba86b028bb0f1fbbc006db5676404ceca58aad9ae3 | C++ | 4,481 | 136 | /*!
* Copyright 2017-2024 by Contributors
* \file updater_quantile_hist.cc
*/
#include <vector>
#include <memory>
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wtautological-constant-compare"
#pragma GCC diagnostic ignored "-W#pragma-messages"
#include "xgboost/tree_updater.h"
#pragma GCC diagnostic ... |
e7b84cad896c696fe354b3b0eb4a9112a4d6662ceca1d844a672eb269f0a6ade | C++ | 4,494 | 165 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
980bd9753f1d9e637058db5862b5f47ce3dd957c9a60e52d903ba7898c94fbed | C++ | 4,503 | 106 | #include "IndexReader.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Parameters.h"
#include "Util.h"
#include <unordered_set>
int mergedbs(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argc, argv, command, t... |
403c6709b07e59a0730dc89d580fc1f53c71c9f9abc53b1755249edb4284e122 | C++ | 4,514 | 119 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "FileUtil.h"
#include "Debug.h"
#ifdef HAVE_ZLIB
#include <zlib.h>
#endif
#ifdef OPENMP
#include <omp.h>
#endif
int unpackdb(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstan... |
2e90b3636b7ec4841f33ad552b44b94c4ccab69e179363d27985d966cd8a24d0 | C++ | 4,519 | 129 | #include "Debug.h"
#include "Parameters.h"
#include "Aggregation.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
class BestHitBySetFilter : public Aggregation {
public :
BestHitBySetFilter(const std::string &targetDbName, const std::string &resultDbName,
const std::string &output... |
133ac4c9524983b425f821f9c11e428a3dedafe387dbb88ef79c376c45e45d38 | C++ | 4,520 | 147 | // This script converts the MNIST dataset to a lmdb (default) or
// leveldb (--backend=leveldb) format used by caffe to load data.
// Usage:
// convert_mnist_data [FLAGS] input_image_file input_label_file
// output_db_file
// The MNIST dataset could be downloaded at
// http://yann.lecun.com... |
0db63e5aae5a192cc27c6388515f81fd2f8758e37ec715f47332cb5284855bc7 | C++ | 4,521 | 119 | #include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "MappingReader.h"
#ifdef OPENMP
#include <omp.h>
#endif
int addtaxonomy(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
... |
de692900e279ad2d8f09de8c0cdbe840bdf742e71f73b637b841b5fee805ac93 | C++ | 4,575 | 142 | #include "mutual_information.h"
#include <algorithm> // std::copy
#include <numeric> // std::iota
#include <Rcpp.h> // Rcpp::stop
namespace miic {
namespace computation {
using structure::TempGrid2d;
using structure::TempVector;
using utility::TempAllocatorScope;
// INPUT
// datafactors: [0, ]: x, [1, ]: y,... |
c06784da2cb8038bbf89c86d9958c8b7f66a3318c2f6f1e432cba586ca9d5e55 | C++ | 4,579 | 125 | #include <iostream>
#include <list>
#include <algorithm>
#include <cmath>
#include "SequenceLookup.h"
#include "SubstitutionMatrix.h"
#include "UngappedAlignment.h"
#include "ExtendedSubstitutionMatrix.h"
#include "FileUtil.h"
#include "kseq.h"
#include <unistd.h> // read
KSEQ_INIT(int, read)
#include "Clustering.h... |
707d7e27668b4708895676b2a1b4dfe6da1d81458da1c838acc2295a742c1f9d | C++ | 4,591 | 182 | #include <sstream>
#include "handler_test.h"
#include "yaml-cpp/yaml.h" // IWYU pragma: keep
#include "gtest/gtest.h"
using ::testing::_;
using ::testing::InSequence;
namespace YAML {
namespace {
typedef void (*EncodingFn)(std::ostream&, int);
inline char Byte(int ch) {
return static_cast<char>(
static_ca... |
a7d5bed60e8b2ab6ad197c8dbcee26d6690fc5de37dfbb4f893f8ce498422256 | C++ | 4,608 | 121 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
05c580a1be471da08b85e7ad63ab75f28b21616181df7d9ac35318fd573a2263 | C++ | 4,647 | 125 | #include "Orf.h"
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "TranslateNucl.h"
#include "FileUtil.h"
#ifdef OPENMP
#include <omp.h>
#endif
int translatenucs(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::ge... |
8719a01dec0a91128db4c24c0c0d76163f3168c4d1682787e02deaca918826d4 | C++ | 4,666 | 146 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include "coll.h"
#include <algorithm> // for min, max, copy_n
#include <cstddef> // for size_t
#include <cstdint> // for int8_t, int64_t
#include <functional> // for bit_and, bit_or, bit_xor, plus
#include <string> // for string
#include <type_... |
0882b35875517de734df734bb30a0c2922903687a9a11dd34cf086c02ae6b4ed | C++ | 4,694 | 126 | #include <algorithm>
#include <vector>
#include "caffe/layers/slice_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void SliceLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dtype>*>& top) {
const SliceParameter& slice_param = thi... |
28ab54722df3011fddfaddf97cbb880058698cdc2a9dee8238330d2406f031f6 | C++ | 4,697 | 156 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* xgeqrf.cpp
*
* Code generation for function 'xgeqrf'
*
*/
/* Include files */
#include "xgeqrf.h"
#include... |
38a9742de4aa7617086a23aceac9986a28827eafd18cc856ed1489fe283d5c01 | C++ | 4,710 | 157 | // Copyright 2006, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
d9155f1b1bf91a0673cd3c6c81590377cb5afbfc63985aba77c86c8f593da35f | C++ | 4,714 | 112 | #include <cassert>
#include "LinsearchIndexReader.h"
#include "PrefilteringIndexReader.h"
#include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
#include "easyrbh.sh.h"
int easyrbh(int argc, const char **argv, const Command &command) {
Parameters &par = Parame... |
8627b21fb60aa0f9fd3c0742e1611940faebb4ff842b43eaa3f6b6d21fbd2a86 | C++ | 4,778 | 136 | /**
* Copyright 2023-2024, XGBoost contributors
*/
#include "federated_comm.h"
#include <grpcpp/grpcpp.h>
#include <cstdint> // for int32_t
#include <cstdlib> // for getenv
#include <limits> // for numeric_limits
#include <string> // for string, stoi
#include "../../src/common/common.h" // for Split
#in... |
177bdca261cfc47c727598be53005a5e558137751f4e9076669c67ec6b034f66 | C++ | 4,785 | 149 | /*
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under both the BSD-style license (found in the
* LICENSE file in the root directory of this source tree) and the GPLv2 (found
* in the COPYING file in the root directory of this source tree).
*/
#include "Pzst... |
aa4eba56539f3393c1c17a718127cc4a200a7fde81fc4900c920a47d233eb7fb | C++ | 4,788 | 215 | /*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either versio... |
ef4ee1600d13f7b45089d50df856203c4ea63941c3ee3dcdbcdbfeabac4fbfc4 | C++ | 4,816 | 102 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <StripedSmithWaterman.h>
#include <MsaFilter.h>
#include "PSSMCalculator.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#include "MultipleAlignment.h"
#... |
2441c5ffc2f6fe1383abc09584872c22e20d4f5929968f6c5d4c807cfcbf7629 | C++ | 4,862 | 119 | /**
* Copyright 2022-2024, XGBoost Contributors
*/
#include "stats.h"
#include <cstddef> // std::size_t
#include <numeric> // std::accumulate
#include "../collective/aggregator.h" // for GlobalSum
#include "linalg_op.h" // for Matrix
#include "optional_weight.h" // OptionalWeights... |
0d9866f1df7a5d2dfa7d77b14362142d413e0a8d7751599694aaeb1c049c1471 | C++ | 4,883 | 141 | #include <iostream>
#include <list>
#include <algorithm>
#include <math.h>
#include <sys/stat.h>
#include <stdio.h>
#include <string.h>
#include "Clustering.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Parameters.h"
const char* binary_name = "test_dbreader_zlib";
//static off_t fsize_orDie(const char *fi... |
245a70b636e93a604eadd42c021ca3fb6751183eb24bcdd009e642288e623ead | C++ | 4,891 | 155 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <numeric> // for iota
#include "../../../src/collective/allreduce.h"
#include "../../../src/collective/coll.h" // for Coll
#include "../../../src/common/type.h" // for EraseType
#include "test_worker.h" // for Work... |
c9aa0cf99af218ed9f933e0de73924419d483eb89a4240c35ee6a3fac96bb160 | C++ | 4,912 | 110 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This... |
4554285c5c2867b601964806cf4ba8ceb24d97ca3d327ea66f680915119f89d8 | C++ | 4,917 | 144 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
db2072877752cbcb71d5f12350e22bf015cda39f1aac5b70279eb6e5917efa67 | C++ | 4,969 | 133 | #include "gmock/gmock.h"
#include <Orf.h>
class OrfTest : public testing::Test {
protected:
const char* sequence = "CGAAGCGGGTGATGGCCGGCGCCGCGCCGGTTGGCGGCTGGCCATTCAAGGAGTGAGGAGATGGTCACTGGGCAGCGCGCCGGGGGGCGGCAGCAGCCCAAGGGTCGGGTCATTCCCGATTGGCCGCACCAGGCGCCCGCCACAGCCGGA";
const char* reverseComplement = "TCCGGC... |
abc8b20689c432d0fbf186638a773be35de9678215926ff751c2ea460879035d | C++ | 4,989 | 129 | #include "stdafx.h"
#include "TestLib.h"
#include "LandauVishkin.h"
// Test fixture for all the Landau-Viskhin Tests
struct LandauVishkinTest {
LandauVishkin<> lv;
LandauVishkinWithCigar lvc;
};
TEST_F(LandauVishkinTest, "equal strings") {
ASSERT_EQ(0, lv.computeEditDistance("abcde", 5, "abcde", 5, 2));
}
... |
2716c1efd81808b58cd00721e97cc8a21e4ea4c4b929c97449ba64dce9515ddd | C++ | 5,002 | 138 | #include <algorithm>
#include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/infogain_loss_layer.hpp"
#include "caffe/test/test_caffe_main.hpp"
#include "caffe/test/test_gradient_check_util.hpp"
namespace caffe {
template <... |
61241c0c055523e5029c8265c4bd7a7fff90d3552752616f7bfb83d1b8ae9d9e | C++ | 5,002 | 93 | #include <Rcpp.h>
#include "tsne.h"
using namespace Rcpp;
Rcpp::List save_results(int N, int no_dims, const std::vector<double>& Y, const std::vector<double>& costs, const std::vector<double>& itercosts,
double theta, double perplexity, int D, int stop_lying_iter, int mom_switch_iter,
double momentum,... |
0b79bc7d46cc633a5dbe4e1cb0e3691b6ba0294ad3608f3c1e723c4ec900cd91 | C++ | 5,017 | 154 | /**
* Copyright 2020-2024 by XGBoost contributors
*/
#include <gtest/gtest.h>
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wtautological-constant-compare"
#pragma GCC diagnostic ignored "-W#pragma-messages"
#include "../../../src/data/gradient_index.h" // for GHistIndexMatrix
#pragma GCC diagno... |
45038800c8818073ba0bfd9a0c40bbbfb3db04989dd26691961ce63c9e685774 | C++ | 5,025 | 153 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include "comm_group.h"
#include <algorithm> // for transform
#include <cctype> // for tolower
#include <chrono> // for seconds
#include <cstdint> // for int32_t
#include <iterator> // for back_inserter
#include <memory> // for shared_ptr, unique_p... |
6df2ec35df46ae9640173358a765239ca0f60be861007aeb86bbb767f39897b3 | C++ | 5,033 | 129 | #include "ExtendedSubstitutionMatrix.h"
#include "Indexer.h"
#include "Util.h"
#include "simd.h"
#include <iterator>
#include <cmath>
#include <cstdlib>
#ifdef OPENMP
#include <omp.h>
#endif
struct sort_by_score {
bool operator()(const std::pair<short,unsigned int> &left, const std::pair<short,unsigned int> &rig... |
cd6aedeaf296331d66de9422d5234d37d9da77cc1ff96cf9bf96e1cdfd19f58b | C++ | 5,045 | 169 | /*!
* Copyright 2021 XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/base.h>
#include <xgboost/tree_model.h>
#include "../helpers.h"
namespace xgboost {
class TestGrowPolicy : public ::testing::Test {
protected:
std::shared_ptr<DMatrix> Xy_;
size_t n_samples_ = 4096, n_features_ = 13;
float... |
f6474ce8ec73d63d07f776bb5dd9fd2b01f0b31a3667f038656dc4ce1ceb55bd | C++ | 5,047 | 192 | /**
* Copyright 2023, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h> // for DeviceOrd
#include <xgboost/data.h> // for DataSplitMode
#include <algorithm> // for min
#include <cstdint> // for int32_t
#include <functional> // for function
#include <string> // for string
... |
dc3352259f5bc5b00c9f1c09545321eab34fa96756e4ce541afee7cb3e10108e | C++ | 5,053 | 144 | // Copyright 2009 Google Inc. All Rights Reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and ... |
660603aabd510de509962fd48018f6cc9c25e4b5c66225b4656c12be3152461a | C++ | 5,069 | 151 | /**
* Copyright 2023, XGBoost contributors
*/
#include "federated_coll.h"
#include <federated.grpc.pb.h>
#include <federated.pb.h>
#include <algorithm> // for copy_n
#include "../../src/collective/allgather.h"
#include "../../src/common/common.h" // for AssertGPUSupport
#include "federated_comm.h" ... |
f9fdc5d2795e600841843d2667214ab8f02d35263cd7d45d6c28afeafd7a8f54 | C++ | 5,114 | 159 | /**
* Copyright 2022-2023 XGBoost contributors
*/
#include <gtest/gtest.h>
#include "../../../src/data/adapter.h"
#include "../../../src/data/simple_dmatrix.h"
#include "../helpers.h"
#include "xgboost/context.h"
namespace xgboost {
namespace {
class DMatrixForTest : public data::SimpleDMatrix {
size_t n_regen_{0... |
9107bbf9b5870c3bebaeb6a68256ab96d8e4c26953c924b7fa70c38c3b37531d | C++ | 5,117 | 159 | // This program converts a set of images to a lmdb/leveldb by storing them
// as Datum proto buffers.
// Usage:
// convert_imageset [FLAGS] ROOTFOLDER/ LISTFILE DB_NAME
//
// where ROOTFOLDER is the root folder that holds all the images, and LISTFILE
// should be a list of files as well as their labels, in the format... |
5fe201b31ac20330ac4eeb72e009c68bac6dda547edc99c0c4cc6a2588d497e3 | C++ | 5,129 | 153 | // Copyright 2005, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
24557f14bfcbb8772467be948a082a6d9abfa740977a164e01b397710c14638c | C++ | 5,175 | 177 | #include "gtest/gtest.h"
#include "regex_yaml.h"
#include "stream.h"
using YAML::RegEx;
using YAML::Stream;
namespace {
const auto MIN_CHAR = Stream::eof() + 1;
TEST(RegExTest, Empty) {
RegEx empty;
EXPECT_TRUE(empty.Matches(std::string()));
EXPECT_EQ(0, empty.Match(std::string()));
for (int i = MIN_CHAR; i ... |
95330a919f37eb505aa37bb370b15cf1e325615387d5ed46c22dee2b06ce6d38 | C++ | 5,195 | 223 | #include "KSeqWrapper.h"
#include "kseq.h"
#include "FileUtil.h"
#include "Util.h"
#include "Debug.h"
#include <unistd.h>
namespace KSEQFILE {
KSEQ_INIT(int, read)
}
KSeqFile::KSeqFile(const char* fileName) {
file = FileUtil::openFileOrDie(fileName, "r", true);
seq = (void*) KSEQFILE::kseq_init(fileno(fil... |
a45f95553de72efcf263f1f5df7c1bfa9d3d0c039bf92f7016bb2b1246cd76a6 | C++ | 5,245 | 176 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "kraken2_headers.h"
#include "compact_hash.h"
#include "taxonomy.h"
#include "mmscanner.h"
#include "kraken2_data.h"
#include "reports.h"
using std::string;
using s... |
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