sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
13d119879df385ac9d4033f3ab943e4377f501eff0f3eeb2ecd5372cd71fa516 | C++ | 2,772 | 107 | /*++
Module Name:
AlignmentResult.cpp
Abstract:
Code for SNAP genome alignment results
Authors:
Bill Bolosky, March, 2015
Environment:
Revision History:
--*/
#include "stdafx.h"
#include "AlignmentResult.h"
#include "GenomeIndex.h"
int
SingleAlignmentResult::compareByContigAndScore(const ... |
621a1e6fa426c1d0438841f76cdfcd23a72b1c597226c150c3da801d1ab024b8 | C++ | 2,803 | 73 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <Rcpp.h>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(... |
295afd48e83d0a1740cabc002a235bd7a4196d9352cf50589014782a789ce60e | C++ | 2,809 | 105 | /**
* Copyright 2015-2024, XGBoost Contributors
* \file logging.cc
* \brief Implementation of loggers.
* \author Tianqi Chen
*/
#include "xgboost/logging.h"
#include <string> // for string
#include "collective/communicator-inl.h"
#if !defined(XGBOOST_STRICT_R_MODE) || XGBOOST_STRICT_R_MODE == 0
// Override log... |
8d0747af4ba9903527d13c281a2dcb11d73d294a4219da632a225439418a4d0b | C++ | 2,809 | 88 | /**
* Copyright 2023 by XGBoost contributors
*/
#include "error_msg.h"
#include <mutex> // for call_once, once_flag
#include <sstream> // for stringstream
#include "../collective/communicator-inl.h" // for GetRank
#include "xgboost/context.h" // for Context
#include "xgboost/logging.h"
namespa... |
30d4384991791629af2b65b2bd79b127ea50edd32bdaa086785373b6951558c8 | C++ | 2,823 | 119 | #include <cassert>
#include <sstream>
#include "yaml-cpp/emitfromevents.h"
#include "yaml-cpp/emitter.h"
#include "yaml-cpp/emittermanip.h"
#include "yaml-cpp/null.h"
namespace YAML {
struct Mark;
} // namespace YAML
namespace {
std::string ToString(YAML::anchor_t anchor) {
std::stringstream stream;
stream << a... |
3c18a4eb8dd71e798a7a3c3bf38548c6f491a21f02c0d245597d59cd9235e3d5 | C++ | 2,829 | 101 | #include "nodeevents.h"
#include "yaml-cpp/eventhandler.h"
#include "yaml-cpp/mark.h"
#include "yaml-cpp/node/detail/node.h"
#include "yaml-cpp/node/detail/node_iterator.h"
#include "yaml-cpp/node/node.h"
#include "yaml-cpp/node/type.h"
namespace YAML {
void NodeEvents::AliasManager::RegisterReference(const detail::no... |
0a3a69816c69f5bafe1d1dc4755f1d9700d203f5085717bea8ce5268970ba010 | C++ | 2,830 | 120 | #include <iostream>
#include <cassert>
#include <tinyexpr.h>
#include <ExpressionParser.h>
#include "Util.h"
#include "TaxonomyExpression.h"
const char* binary_name = "test_taxexpr";
int main (int, const char**) {
std::string path = "/Users/mad/Documents/databases//swissprot/sprot_new";
NcbiTaxonomy *taxono... |
8882e89bb8669775d594ec8159418a60339672b0616e0de63968397576ba1361 | C++ | 2,831 | 94 | /**
* Copyright 2019-2023, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/base.h>
#include <xgboost/logging.h>
#include <memory>
#include <string>
#include "../../../src/tree/constraints.h"
#include "../../../src/tree/hist/evaluate_splits.h"
#include "../helpers.h"
namespace xgboost::tree {
TES... |
b25ba9dd9d11e98ec86a1fc7ab0268b58d9d1eea5af7eccd72bb8a2881d9cb3d | C++ | 2,847 | 71 | /**
* Copyright 2021-2024, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h> // for Context
#include <cstddef> // for size_t
#include <memory> // for unique_ptr
#include "../../../src/common/column_matrix.h" // for common::ColumnMatrix
#include "../../../src/common/io.h" ... |
2258164e0421d333839a7086eefcbdcf791ecf0433f50d92a0b8cf13c7a95df3 | C++ | 2,849 | 78 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h> // for Context
#include <xgboost/multi_target_tree_model.h>
#include <xgboost/tree_model.h> // for RegTree
namespace xgboost {
namespace {
auto MakeTreeForTest() {
bst_target_t n_targets{3};
bst_feature_... |
738a1039c30c5d2f14b49b2e9f052a22d7313b7bde6fd92fe18a975a04532877 | C++ | 2,867 | 109 | /*++
Module Name:
SeedSequencer.cpp
Abstract:
Code for determining the order of seeds in a read.
Authors:
Bill Bolosky, August, 2013
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "SeedSequencer.h"
static SeedSequencer *Sequencers[LargestSeedSize + 1... |
3cf998380edf6c5b916840fad5dbcbb4fba04915d609d67363ee5ba3f3af1e73 | C++ | 2,873 | 79 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#include "itoa.h"
#ifdef OPENMP
#include <omp.h>
#endif
int profile2neff(int argc, const char **argv, const Command &command) {
Parameters &par = Parameter... |
633592c347d5ea7861b0cd5cc5682c132e12e254a334122165e1e71c92f45383 | C++ | 2,876 | 92 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include "Sequence.h"
#include "Indexer.h"
#include "ExtendedSubstitutionMatrix.h"
#include "SubstitutionMatrix.h"
#include "Reduce... |
0c8109372c6b99cd6861eb114d56ff31afd3db13d5a24feb575e72330f3ea1ef | C++ | 2,878 | 75 | /**
* Copyright 2019-2025, XGBoost Contributors
*/
#include "adapter.h"
#include <utility> // for move
#include "../c_api/c_api_error.h" // for API_BEGIN, API_END
#include "array_interface.h" // for ArrayInterface
#include "xgboost/c_api.h"
#include "xgboost/logging.h"
namespace xgboost::data {
ColumnarAd... |
c7522a9b9554591bddbf83923e4ff159adea67b5a4688a2821fcdad32851ac6c | C++ | 2,882 | 87 | /**
* Copyright 2023, XGBoost Contributors
*/
#include "broadcast.h"
#include <cmath> // for ceil, log2
#include <cstdint> // for int32_t, int8_t
#include <utility> // for move
#include "../common/bitfield.h" // for TrailingZeroBits, RBitField32
#include "comm.h" // for Comm
#incl... |
3093c6f0e067a708e3efbb68fb3648068fff6885cb784c993a9bee5af1c754d7 | C++ | 2,913 | 78 | #include "Parameters.h"
#include "FileUtil.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "IndexReader.h"
#include "NucleotideMatrix.h"
#include <climits>
#ifdef OPENMP
#include <omp.h>
#endif
int countkmer(int argc, const char **argv, const Command& command) {
Param... |
3459fee867a65016716e76e61834e7da843aa4fdf9de54010456d03b5ca66d7b | C++ | 2,913 | 103 | /*
* 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... |
c6d7b92f8fa6d1bf252da90a9b0f1f830f5173ccca180e2dcf828d4b0ba7c068 | C++ | 2,931 | 99 | /*
* 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
* ... |
9487f41d50366f53e18d8516f1dc2f96cdf8a508f393beb1fa364314384cf071 | C++ | 2,933 | 115 | #include <boost/bind.hpp>
#include <glog/logging.h>
#include <signal.h>
#include <csignal>
#include "caffe/util/signal_handler.h"
namespace {
static volatile sig_atomic_t got_sigint = false;
static volatile sig_atomic_t got_sighup = false;
static bool already_hooked_up = false;
void handle_signal(int signal... |
a73c9d44f10e7f923e328838e685309eeaac2f510468d1d171ca958c7fbee8e5 | C++ | 2,957 | 75 | /**
* Copyright 2017-2024 by Contributors
*/
#include "xgboost/predictor.h"
#include <dmlc/registry.h> // for DMLC_REGISTRY_LINK_TAG
#include <cstdint> // for int32_t
#include <string> // for string, to_string
#include "../gbm/gbtree_model.h" // fo... |
cd72e82b9cd04859fbecfe641aa558ad3b1794e811192642173cea3c0833a338 | C++ | 2,970 | 71 | #include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "IndexReader.h"
#ifdef OPENMP
#include <omp.h>
#endif
int mergeresultsbyset(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, tru... |
d165f344577c2c0a15dc9e3a7692907829228ec480af0fac26647ac52e03be9f | C++ | 2,977 | 89 | /**
* Copyright 2018-2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/data.h>
#include <xgboost/host_device_vector.h>
#include <xgboost/learner.h>
#include <xgboost/tree_updater.h>
#include <memory>
#include <string>
#include <vector>
#include "../../../src/tree/param.h" // for TrainParam... |
1606495746de0858960a76660399a1177bb6a97cf940c6b5c66fb4921d0fd5c3 | C++ | 2,980 | 97 | /*
* 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.
*
* repmat.cpp
*
* Code generation for function 'repmat'
*
*/
/* Include files */
#include "repmat.h"
#include... |
9caf610068242de20b5d92082c9888de03558eb11f79910bb9f29ab8574dfa7c | C++ | 3,034 | 129 | #include <cstdio>
#include <sstream>
#include "directives.h" // IWYU pragma: keep
#include "scanner.h" // IWYU pragma: keep
#include "singledocparser.h"
#include "token.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
#include "yaml-cpp/parser.h"
namespace YAML {
class EventHandler;
Parser::Parser() {}... |
772d9dc3df628fef9dc894e3c1b7813f5547441b08500e8d432ff3befd894473 | C++ | 3,043 | 88 | /**
* Copyright 2021-2024, XGBoost Contributors
*/
#include "proxy_dmatrix.h"
#include <memory> // for shared_ptr
#include "xgboost/context.h" // for Context
#include "xgboost/data.h" // for DMatrix
#include "xgboost/logging.h"
#include "xgboost/string_view.h" // for StringView
#if !defined(XGBOOST_USE_CUD... |
42054e139fbd6dd2a32bb41a88b9b5d8550771331bd022ce3b4e52a5f24be87a | C++ | 3,047 | 81 | // Computes either a PSSM or a MSA from clustering or alignment result
// For PSSMs: MMseqs just stores the position specific score in 1 byte
#include "CSProfile.h"
#include "MathUtil.h"
#include "DBReader.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "Masker.h"
#include "simd.h"
#include <string>
#ifd... |
39773d691b10ee0c6abcd3ee647f13022518c1a36f3979092fe6400134f79306 | C++ | 3,052 | 89 | #include <cmath>
#include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/euclidean_loss_layer.hpp"
#include "caffe/test/test_caffe_main.hpp"
#include "caffe/test/test_gradient_check_util.hpp"
namespace caffe {
template <typ... |
f8d2c48cbd4dfe0fe11b7ae48abd1889c7c4e5f54137bdfb0eb7293293ea51e0 | C++ | 3,057 | 80 | #include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
int result2rbh(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
DBReader<DBKeyTyp... |
4a292e04e39082f2d465adcab49cb8d0eae6e8af31980a817c7761a7506f03cb | C++ | 3,064 | 85 | #include "Parameters.h"
#include "Util.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "HeaderSummarizer.h"
#include <sstream>
#ifdef OPENMP
#include <omp.h>
#endif
int summarizeheaders(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
... |
1f8f1ea44e0937d93667b4d46ba21dcea59ccbfdd55215e2932d100ec02deb1f | C++ | 3,094 | 101 | #include "Parameters.h"
#include "DBReader.h"
#include "Debug.h"
#include "Util.h"
#include "microtar.h"
#ifdef HAVE_ZLIB
#include <zlib.h>
static int file_gzwrite(mtar_t *tar, const void *data, size_t size) {
size_t res = gzwrite((gzFile)tar->stream, data, size);
return (res == size) ? MTAR_ESUCCESS : MTAR_E... |
ca50f99174dd9852fd1e83001ed71d798b8e0c5945159df8b3259b106c2daa1d | C++ | 3,103 | 130 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 2022 Matteo Cartiglia - University of Zurich
Copyright (C) 2022-2023 Ole Richter - University of Groningen
This program is free software: you can redistribute it and/or modify
it under the... |
04ccf832cf86c9b308288d30cdb04a1e9f0f46cfbcf0dc81938d94275c974ddf | C++ | 3,104 | 72 | // 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 ... |
227d27ffbdcbc6abbb0a7d6151cbd73cd2097d2e3064e618850417fd26adfde8 | C++ | 3,105 | 70 | /**
* Copyright 2021-2024, XGBoost Contributors
*/
#include "gradient_index_page_source.h"
#include <memory> // for make_shared
#include <utility> // for move
#include "../common/hist_util.h" // for HistogramCuts
#include "gradient_index.h" // for GHistIndexMatrix
namespace xgboost::data {
void GradientI... |
6a25b8afcf5ec26084d16756ebdc47009f9b1890c0130bb399058ccff97910a8 | C++ | 3,106 | 81 | /**
* Copyright 2022-2024, XGBoost Contributors
*
* @brief Utilities for estimating initial score.
*/
#include "fit_stump.h"
#include <cstddef> // std::size_t
#include <cstdint> // for int32_t
#include "../collective/aggregator.h" // for GlobalSum
#include "../common/threading_utils.h" // ParallelFor
#includ... |
7d4131eafc4221eb8218cbf37ae9b5ac736deac329449563f5b0d5c839b56c6e | C++ | 3,108 | 83 | #include <vector>
#include "caffe/layers/deconv_layer.hpp"
namespace caffe {
template <typename Dtype>
void DeconvolutionLayer<Dtype>::compute_output_shape() {
const int* kernel_shape_data = this->kernel_shape_.cpu_data();
const int* stride_data = this->stride_.cpu_data();
const int* pad_data = this->pad_.cpu_... |
ad19864cb6f02fa92210e30abd2dea96f4b99c928b6b5cf0191aa08d685ae6ce | C++ | 3,113 | 92 | #include "SubstitutionMatrix.h"
#include "Sequence.h"
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "TranslateNucl.h"
#ifdef OPENMP
#include <omp.h>
#endif
int translateaa(int argc, const char **argv, const Command &command) {
Parameters &par = P... |
6fd05d2161408091de53cbb56633af2960a36cc54cbd3cf830e7b96782687f2f | C++ | 3,116 | 82 | #include "Parameters.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "CommandCaller.h"
#include "enrich.sh.h"
#include <cassert>
void setEnrichWorkflowDefaults(Parameters *p) {
p->numIterations = 3;
p->expansionMode = 1;
}
int enrich(int argc, const char **argv, const Command &command... |
738def9ff66573665dda694bedc7492b6f991770954e8259063dee0db13e9eff | C++ | 3,119 | 85 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include "Sequence.h"
#include "Indexer.h"
#include "ExtendedSubstitutionMatrix.h"
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "KmerGenerator.h"
#i... |
0f9eed9816768bae2342b3815a33034351fda195d7e4b29f36586654e8c94216 | C++ | 3,125 | 117 | /*
* 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.
*
* find.cpp
*
* Code generation for function 'find'
*
*/
/* Include files */
#include "find.h"
#include "eml_... |
c7d503543bee6ec97575e73762cbd3de4e7163992941bd9fb64d781e2163b9cb | C++ | 3,127 | 134 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "mmap_file.h"
using std::string;
namespace kraken2 {
MMapFile::MMapFile() {
valid_ = false;
fptr_ = NULL;
filesize_ = 0;
fd_ = -1;
}
void MMapFile::OpenF... |
89db10c5ea60d1e7d475c29f1cc6a744b777c41cac2888b5ed3c85b4c594668a | C++ | 3,139 | 76 | // dear imgui: wrappers for C++ standard library (STL) types (std::string, etc.)
// This is also an example of how you may wrap your own similar types.
// Compatibility:
// - std::string support is only guaranteed to work from C++11.
// If you try to use it pre-C++11, please share your findings (w/ info about compil... |
393e027e24d66a22e4c6ceb3f56bd05ac8c276abeaefad44c5326eaff01eaeb9 | C++ | 3,147 | 128 | #include "scanner.h"
#include "token.h"
namespace YAML {
struct Mark;
Scanner::SimpleKey::SimpleKey(const Mark& mark_, std::size_t flowLevel_)
: mark(mark_), flowLevel(flowLevel_), pIndent(0), pMapStart(0), pKey(0) {}
void Scanner::SimpleKey::Validate() {
// Note: pIndent will *not* be garbage here;
// ... |
1278c151a2db0be7b8fa14ac5641fff1519322a3b3a003df9fd73d8d450f3ebd | C++ | 3,149 | 113 | #ifdef USE_LMDB
#include "caffe/util/db_lmdb.hpp"
#include <sys/stat.h>
#include <string>
namespace caffe { namespace db {
void LMDB::Open(const string& source, Mode mode) {
MDB_CHECK(mdb_env_create(&mdb_env_));
if (mode == NEW) {
CHECK_EQ(mkdir(source.c_str(), 0744), 0) << "mkdir " << source << " failed";
... |
57df73c2b055feae22d2ac5b6724830e87be297952cdfc8a87a2c197bb3ce2e3 | C++ | 3,149 | 130 | #include <assert.h>
#include <cassert>
#include "nodebuilder.h"
#include "yaml-cpp/node/detail/node.h"
#include "yaml-cpp/node/impl.h"
#include "yaml-cpp/node/node.h"
#include "yaml-cpp/node/type.h"
namespace YAML {
struct Mark;
NodeBuilder::NodeBuilder()
: m_pMemory(new detail::memory_holder), m_pRoot(0), m_map... |
1afde5050ce356649b63cfc0fb214690e421bf28b637200d2fbd7fece3477906 | C++ | 3,166 | 90 | /**
* Copyright 2015-2023, XGBoost Contributors
* \file custom_metric.cc
* \brief This is an example to define plugin of xgboost.
* This plugin defines the additional metric function.
*/
#include <xgboost/base.h>
#include <xgboost/parameter.h>
#include <xgboost/objective.h>
#include <xgboost/json.h>
namespace xg... |
3d6134d10e7bc10cc1cdb49f11629b8917e4b3e999a332acc1ac1f9dadffe642 | C++ | 3,172 | 89 | #include "Parameters.h"
#include "Util.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "MathUtil.h"
#include "Matcher.h"
#ifdef OPENMP
#include <omp.h>
#endif
int summarizealis(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.p... |
101fd45ecb209961bf39fdb8919255de3e5108ba27d4ba0b8bfedf5d385a7e2a | C++ | 3,175 | 106 | #include "stdafx.h"
#include "KuString.h"
#include "StringConv.h"
#include "util.h"
#ifdef _WIN32
LPCWSTR StringUTF8ToWChar(LPCSTR sUTF8, CStringW &sWChar, int iChars/* = -1*/)
{
if (!sUTF8)
return NULL;
sWChar.Empty();
int iLen = MultiByteToWideChar(CP_UTF8, 0, sUTF8, iChars, NULL, 0);
if (iLen > 0) {
LPWSTR... |
9dde00dd6326dd87f7dd8c603f4e2c83e91e11754ec9b5326aef2f6c43eea27c | C++ | 3,175 | 90 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "Matcher.h"
#include "QueryMatcher.h"
#include "FastSort.h"
#ifdef OPENMP
#include <omp.h>
#endif
int sortresult(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::ge... |
c6317aed7e98a1d51acdd7500b77a5c945e40b123c15a1f59c7660deab6a0d71 | C++ | 3,177 | 93 | #include "yaml-cpp/binary.h"
namespace YAML {
static const char encoding[] =
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
std::string EncodeBase64(const unsigned char *data, std::size_t size) {
const char PAD = '=';
std::string ret;
ret.resize(4 * size / 3 + 3);
char *out = &ret[0]... |
474390ad57d09c90b664426aa2e24faeeec52ae67121ac1a49526640ba0057eb | C++ | 3,205 | 83 | /* coding=utf-8
* Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*... |
9b610c84f60a049d83b7294357c87dbd05c39f3932bd8dc1ebc9e8bdc95d0a4d | C++ | 3,218 | 155 | /*
* 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... |
0140c3aeea4c0ad932503dab0406c9562c4618e500ab52e592a8a01fd02841da | C++ | 3,231 | 123 | /*
* Copyright (C) 2019-2024 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... |
3d7f91430b6cb1c0645709f4994ee7157461701241ddf8c0c429172e0ba060d8 | C++ | 3,235 | 106 | #include <map>
#include <string>
#include "kraken2_data.h"
#include "taxonomy.h"
using namespace kraken2;
extern "C" {
Taxonomy *init_taxonomy(const char *filename) {
Taxonomy *t = new Taxonomy(filename, false);
t->GenerateExternalToInternalIDMap();
return t;
}
taxid_t get_lca(Taxonomy *t, taxid_t... |
3ca2164fbec8c1caaf8111aafa27475f1b37be6e275ea51f3a3d872dd87106f4 | C++ | 3,260 | 136 | #include <sstream>
#include "exp.h"
#include "stream.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
namespace YAML {
struct Mark;
} // namespace YAML
namespace YAML {
namespace Exp {
unsigned ParseHex(const std::string& str, const Mark& mark) {
unsigned value = 0;
for (std::size_t i = 0; i < str.size... |
1da12e4bdda2a0bc7b59d4638fe34b2d3798134224fd9237eeebdd09c3326011 | C++ | 3,263 | 88 | // 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 ... |
1fc8bc64af9ac9a73327f797b5efa578f684e3a34e05df9fb3ce4126978d6157 | C++ | 3,273 | 100 | // 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 ... |
ff729c128fda7d768809800f7faddf6715d9970fde5442e37edf7dffab020d6a | C++ | 3,283 | 91 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#include "itoa.h"
#ifdef OPENMP
#include <omp.h>
#endif
int profile2pssm(int argc, const char **argv, const Command &command) {
Parameters &par = Parameter... |
1855e86520ac791e41715ee9bf96f4eac6b954f83e6e9c2d29b602f5a48ae4dd | C++ | 3,284 | 139 | /*
* 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... |
737995b37dad3ca10c913cc466860e7ac340f690549023fccb673366ba9b3612 | C++ | 3,296 | 81 | #include <iostream>
#include <list>
#include <algorithm>
#include <cmath>
#include "SequenceLookup.h"
#include "SubstitutionMatrix.h"
#include "Clustering.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Parameters.h"
const char* binary_name = "test_sequenceindex";
DEFAULT_PARAMETER_SINGLETON_INIT
int main (... |
eac4f692b2b53d91e08a03f1c6a80e05639b05a9c709f10783032307d7622b58 | C++ | 3,306 | 103 | // 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 ... |
f8a541bd63b465d50c0997c0d3e449ef0498ed02282a7e3deeb0fe9f7d95900f | C++ | 3,318 | 72 | #include "Parameters.h"
#include "Util.h"
#include "PrefilteringIndexReader.h"
#include "MemoryMapped.h"
#include <sys/mman.h>
int touchdb(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
const char* ... |
504b09f3987f971c0b095ac98f24666120a24aa97758edd9137ed74608dc61d9 | C++ | 3,323 | 81 | // 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 ... |
3ed81b776e7bbca8fc8e87c40a2c97c79180a109f1e6486a10deec4de6758a64 | C++ | 3,329 | 106 | /*
* Copyright (C) 2025-2026 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... |
f7e958be4e189396f8a827f97f452b3cb056286843c2eeb1a25c28525a29a08e | C++ | 3,340 | 136 | /*
* Copyright (C) 2020-2026 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... |
75bc442fc532654dacd497c72348fa8c60a5d12bfe822bceec2cf16d85fa13b4 | C++ | 3,342 | 96 | /**
* Copyright 2014-2023 by XGBoost Contributors
* \file updater_prune.cc
* \brief prune a tree given the statistics
* \author Tianqi Chen
*/
#include <xgboost/tree_updater.h>
#include <memory>
#include "../common/timer.h"
#include "./param.h"
#include "xgboost/base.h"
#include "xgboost/json.h"
namespace xgboos... |
21898f6699c05445c5b090f1f910a0a7eb3726f9b05cf6d25b5f67142de1fbdb | C++ | 3,369 | 110 | /*!
* Copyright 2017-2023 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/predictor.h>
#pragma GCC diagnostic pop
#pragma GCC diagnostic push
#pragma GCC... |
5274d9710392d88a088963b45a992683fef883d91c3d2ae10e44d84a613b1891 | C++ | 3,390 | 123 | /*
* 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
* ... |
24c72ce764c4aa3686c1dd308671e31f2fdf84b9670e6a845f64d9001a129cb8 | C++ | 3,392 | 132 | /*
* 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
* ... |
bd852b5997b1d8560b0a0f03f522ed6b1e44bd9ddbb6f6bdfb1c01b77f0bd0a9 | C++ | 3,393 | 93 | #include "cycle_tracker.h"
#include <algorithm> // std::sort, std::none_of
#include <set>
#include <tuple> // std::tie
#include "linear_allocator.h"
#include "structure.h"
namespace miic {
namespace reconstruction {
namespace detail {
using structure::TempVector;
using utility::TempAllocatorScope;
bool CycleTrac... |
9fbb6cfe607ebe5c4d97dee64ca3d386ad4ccc26ae263ef9e2a43252d1eacc6e | C++ | 3,396 | 85 | #include "Parameters.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "CommandCaller.h"
#include "multihitsearch.sh.h"
void setMultiHitSearchWorkflowDefaults(Parameters *p) {
p->sensitivity = 5.7;
// TODO: Check query cov maybe?
// p->covThr = 0.7;
p->evalThr = 100;
// TODO:... |
2fa082d7e0e65a0341d9d0ef3fabe50f8ef72ea855f2e9381b40effac9c8cc26 | C++ | 3,397 | 101 | /**
* Copyright 2023-2025, XGBoost Contributors
*/
#include "batch_utils.h"
#include <algorithm> // for max
#include <cstddef> // for size_t
#include <cstdint> // for int64_t
#include <utility> // for pair
#include "../common/common.h" // for AssertGPUSupport
#include "../common/cuda_rt_utils.h" ... |
1f0c52da7ecfe05031cf176485da8a66f6a3936f7e6873cbfbf7bd4c5a7fa3ce | C++ | 3,413 | 60 | #include "stdafx.h"
#include "TestLib.h"
#include "AffineGap.h"
#include "LandauVishkin.h"
// Test fixture for all the affine gap tests
struct AffineGapTest {
AffineGap<> ag;
AffineGapTest() : ag(1, 4, 6, 1) {
initializeLVProbabilitiesToPhredPlus33();
}
int editDist;
};
/*
TEST_F(AffineGapTe... |
abc9d35fcf0f52dec23d316e3c3b10c2586413a50b37356c7b04c8e612d3b86a | C++ | 3,431 | 127 | #include "../include/NvFlexExt.h"
#include "../core/maths.h"
namespace
{
// internal version of the public NvFlexExtMovingFrame type
// this must be a byte exact copy of of NvFlexExtMovingFrame
// we just separate the internal types to avoid exposing
// our math types on the API
struct MovingFrame
{
Vec3 positio... |
52269a4be93c7ee96a62ae64417c5025c98a188f6f3da140a312bce90e9e2d4f | C++ | 3,463 | 93 | /**
* Copyright 2022-2023, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/span.h> // for Span
#include <array> // for array
#include "../../../../src/common/type.h" // for EraseType
#include "../../collective/test_worker.h" // for SocketTest
#include "federated_coll.h" // for... |
4a1311ef5d078e10d55a8931acd9e0fbe61ac020505a844e6f3e8bb8b4766c6a | C++ | 3,471 | 109 | /*
* 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.
*
* warning.cpp
*
* Code generation for function 'warning'
*
*/
/* Include files */
#include "warning.h"
#incl... |
6534d6ab1ac9d2f542a08fabe2ce0fdf634391b1f61a91a4a127cc346ab8256e | C++ | 3,471 | 137 | /*
* 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
* ... |
d9772881b6369e569278c8eb4dafd7bba7928bbbd63a26285479d05fb0c3c0c0 | C++ | 3,474 | 109 | /*
* 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.
*
* fft.cpp
*
* Code generation for function 'fft'
*
*/
/* Include files */
#include "fft.h"
#include "FFTWApi... |
11513e8cfa61356bdffe9e3778c0d3b84c694e60ed0e3abe44e0f5d6dbc56fc5 | C++ | 3,512 | 115 | #include "edit_dist.h"
int scutil::hamming_distance(const std::string &A, const std::string &B)
{
int dist = 0;
for (int i = 0; i < B.length(); ++i)
{
dist += (A[i] != B[i]);
}
return dist;
}
double scutil::edit_distance(const std::string& A, const std::string& B)
{
int NA = A.size();... |
56606231905325ebadae120516082a87ea6ff3e2f0e9cbcda45ac32641a46463 | C++ | 3,515 | 93 | // 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... |
6228ff658b4dba1f7d2969ef28de16c98ebfe614267931ce228dcfbbad454b26 | C++ | 3,516 | 125 | #include <vector>
#include "gtest/gtest.h"
#include "caffe/common.hpp"
#include "caffe/syncedmem.hpp"
#include "caffe/util/device_alternate.hpp"
#include "caffe/util/math_functions.hpp"
#include "caffe/test/test_caffe_main.hpp"
namespace caffe {
class SyncedMemoryTest : public ::testing::Test {};
TEST_F(SyncedMem... |
8a918505ad633e5b035d6c326072b7652f243df7c3a07684a9a07447e853aac1 | C++ | 3,517 | 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
* ... |
c3d3f2eb9640c42cc8de3f33d2d249d404f4feb1e5022b06a6704ab68387d2de | C++ | 3,520 | 109 | #include "stdafx.h"
#include "Tables.h"
static const Tables tables;
const char *COMPLEMENT = tables.getComplement();
const char *IS_N = tables.getIsN();
const int *BASE_VALUE = tables.getBaseValue();
const int *BASE_VALUE_NO_N = tables.getBaseValueNoN();
const char *VALUE_BASE = tables.getValueBase();
const unsign... |
fc98a593aecf84bec27cd711e578b8c197fce70f282573e8ec7fa241f228a80d | C++ | 3,536 | 97 | /**
* Copyright 2022-2024, XGBoost contributors
*/
#include <gmock/gmock.h>
#include <gtest/gtest.h>
#include <string> // for string
#include <thread> // for thread
#include "../../../../plugin/federated/federated_comm.h"
#include "../../collective/test_worker.h" // for SocketTest
#include "../../helpers.h" ... |
2a2884afb9a575bbc202df17a4284f46594a0beb0788743720a2d1d27dc7ee13 | C++ | 3,559 | 129 | //
// Created by mad on 11/29/16.
//
#include "LibraryReader.h"
#include <cstring>
#include "Debug.h"
// Returns pointer to first non-white-space character in str OR to NULL if none
// found
const char* LibraryReader::strscn(const char* str) {
if (!str) return NULL;
const char* ptr = str;
while (*ptr != '\... |
180255f0bda58120d3a43630618cf7598a767303b6e36b004b3c7bf36351ddc4 | C++ | 3,565 | 110 | #include "Debug.h"
#include "Parameters.h"
#include "FileUtil.h"
#include "NcbiTaxonomy.h"
int createbintaxonomy(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, false, 0, 0);
NcbiTaxonomy taxonomy(par.db1, par.db2,... |
866af09db34cdf63a684cc9c9841fc9004f3caaa459af6b1aed36fcaa82b0264 | C++ | 3,577 | 121 | // 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... |
d0420721c9f2fd13fd99e82faba4c0ac8eb4334c3eaa9f1a0d4e7b3f4895ad66 | C++ | 3,579 | 85 | #include <cassert>
#include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
#include "easycluster.sh.h"
void setEasyClusterDefaults(Parameters *p) {
p->spacedKmer = true;
p->removeTmpFiles = true;
p->covThr = 0.8;
p->evalThr = 0.001;
p->create... |
2952862c01a38e8074a62f9cb999871980e11c79d0fcad77dfd332b3a43cc5de | C++ | 3,590 | 96 | #include <gtest/gtest.h>
#include <algorithm>
#include "helpers.h"
#include "../../src/data/array_interface.h"
namespace xgboost {
TEST(RandomDataGenerator, DMatrix) {
size_t constexpr kRows { 16 }, kCols { 32 };
float constexpr kSparsity { 0.4f };
auto p_dmatrix = RandomDataGenerator{kRows, kCols, kSparsity}.G... |
a6f36c0c33b24d69bda937c2a0dd2de91cdbc1de2883df381642a1518dc4c475 | C++ | 3,600 | 109 | #include <string>
#include <fstream>
#include <climits>
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
int maskbygff(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
... |
2b54e9436319f8226fc39873d8af0c2209f35bee88de2b845f17d74246aef18c | C++ | 3,625 | 125 | #include <stdint.h>
#include <algorithm>
#include <string>
#include <utility>
#include <vector>
#include "boost/scoped_ptr.hpp"
#include "gflags/gflags.h"
#include "glog/logging.h"
#include "caffe/proto/caffe.pb.h"
#include "caffe/util/db.hpp"
#include "caffe/util/io.hpp"
using namespace caffe; // NOLINT(build/name... |
38d1920879c4aa8af46d45c2ce03d0b96d82ea0a867561b6afa71fcf1f7030e4 | C++ | 3,645 | 141 | /*
* 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
* ... |
dc10869fe545df01db84220471cdd602b6388e0ce1be98e17184e405156a1fdf | C++ | 3,654 | 104 | /**
* Copyright 2016-2023 by XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h>
#include <xgboost/objective.h>
#include "../helpers.h"
#include "../objective_helpers.h"
TEST(Objective, UnknownFunction) {
xgboost::ObjFunction* obj = nullptr;
xgboost::Context tparam;
std::vector<std::... |
810651939aba7baff5a840d274c9fe9c823941c6f4679f57f5977acd6b2ccaa6 | C++ | 3,677 | 110 | //
// This script converts the CIFAR dataset to the leveldb format used
// by caffe to perform classification.
// Usage:
// convert_cifar_data input_folder output_db_file
// The CIFAR dataset could be downloaded at
// http://www.cs.toronto.edu/~kriz/cifar.html
#include <fstream> // NOLINT(readability/streams)
#... |
7b5fe004c4612364949570cc00587a7d5c3fe8a7e654125a5a79acf6d14317a3 | C++ | 3,678 | 91 | #include "Aggregation.h"
#include "Util.h"
#include "Debug.h"
#ifdef OPENMP
#include <omp.h>
#endif
Aggregation::Aggregation(const std::string &targetDbName, const std::string &resultDbName,
const std::string &outputDbName, unsigned int threads, unsigned int compressed)
: resultDbName... |
613ccf50a3ff8f84c975a13e86ea01ea4e36933072388a3738b4acf9ed3ed7cf | C++ | 3,679 | 93 | // Copyright 2010, 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 ... |
3557c576b87b5ddd7174d890f53eb90744fd3f7f7af8ca244ebda0afb17e9485 | C++ | 3,685 | 152 | /*++
Module Name:
AlignerStats.cpp
Abstract:
Common statistics for running single & paired alignment.
Authors:
Ravi Pandya, May, 2012
Environment:
User mode service.
Revision History:
Integrated from SingleAligner.cpp & PairedAligner.cpp
--*/
#include "stdafx.h"
#include "options.h"
#inc... |
d89745e3345d8828f06bbc46bc7084b9a540ccb65243c7a101fe69c08913a5fe | C++ | 3,685 | 98 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#include <sstream>
#ifdef OPENMP
#include <omp.h>
#endif
int addid(const std::string &db1, const std::string &db1Index, const std::string &db2, const std::string &db2Index,
const bool tsvOut, const std::string &m... |
495dfd9167e45d18bdc9b0037868e802dbee5f62eb94ad0cec21a748fd7fca7c | C++ | 3,688 | 80 | #include "Parameters.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "CommandCaller.h"
#include "easytaxonomy.sh.h"
void setEasyTaxonomyDefaults(Parameters *p) {
p->removeTmpFiles = true;
p->createdbMode = Parameters::SEQUENCE_SPLIT_MODE_SOFT;
p->writeLookup = false;
}
void setEasyTa... |
6a1974d2ffc23d37b14149cb24fa9969f9740cbf65479ff0580cf61357ba4049 | C++ | 3,695 | 139 | /*
* 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
* ... |
109694ea493dd8be05317a6eb874edad1b6f79d09104167036b0ef49fc969dcd | C++ | 3,702 | 108 | #include "Util.h"
#include "Parameters.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#include "StripedSmithWaterman.h"
#include <sys/time.h>
#ifdef OPENMP
#include <omp.h>
#endif
const char* binary_name = "test_ungappedcpuperf";
DEFAULT_PARAMETER_SINGLETON_INIT
#define AA_ALPHABET "ACDEFGHIKLMNPQRSTVWY"
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.