sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d87ff63b0e28b7991f19adacaa4662ab25c93fcf9d37f3a40ce017193cbd5d62 | C++ | 14,934 | 470 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// basic_oarchive.cpp:
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http:/... |
b737f60d441ebdbdcbb526b76d934090a2b6ba4074f27ae19924d81dcb948640 | C++ | 14,968 | 469 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// basic_oarchive.cpp:
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http:/... |
e01a3157d3bfb8b09b104546fa3a3895daacab5d4a859adf1d3f5a36a22d5be8 | C++ | 14,987 | 377 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
#include <boost/beas... |
938b2d86f1f7b185c7096ac53926a50eaed974f3b4ff13b0e75fa778c991add9 | C++ | 15,106 | 528 | //
// thread_pool.cpp
// ~~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests... |
a147984811c7815f9e3121c5a8242025c5a74ccd788eb8d223265a0ab7f30a87 | C++ | 15,114 | 590 | /**
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include "dictionary.h"
#include <assert.h>
#include <algorithm>
#include <cmath>
#include <fstream>
#include ... |
46052435403cf5e73550f0f430a9b4751713127ff4a51da6fa50dd06e8927348 | C++ | 15,194 | 500 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
e63c6fbd2ea990985f4ac7e38ac0fcc601034c22a070afb15918e10a03b97ee1 | C++ | 15,362 | 539 |
#ifndef _ENCOMPINTERFACE
#define _ENCOMPINTERFACE
#include "SphereInterpolator.cpp"
class EnergyComputerBase
{
public:
REAL *dataimg;
const int *datasz;
SphereInterpolator *sinterp;
ParticleGrid<Particle> *pcontainer;
int w,h,d;
REAL voxsize_w;
REAL ... |
e094bb237d576cff069979c1cca6a0c66053244c4ae658b302a7a8d3add85902 | C++ | 15,364 | 473 | /**
* @file searches.cc
*
* Implement the BGL dfs and bfs wrappers.
*/
/*
* David Gleich
* 19 April 2006
*/
/*
* 18 April 2007
* Added src/dst pairs to all algorithms to stop searches early.
* Corrected small documentation bugs.
*
* 9 July 2007
* Switched to simple_csr_matrix graph type
*
* 29 August 2... |
177247c017eedbe08f89aa76e443f737e5d3364b8b2ffb14700dcc50fde2745a | C++ | 15,379 | 493 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
//------------------... |
d2d5895644a5177e7784842f26aa2245e46533f23744284436e26de5c8b4772e | C++ | 15,399 | 549 | //
// prefer_only.cpp
// ~~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests... |
c32698b66859027022749426b0e443e6b53aa98da965678386ba5210b5f117fe | C++ | 15,438 | 458 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
41d9927f0da577644313cf0f88dc84c7ad68074bdc608f3f3fb3323c3abc727f | C++ | 15,491 | 449 | #include "mex.h"
#include "cokus.cpp"
// Syntax
// [ WP , AT , Z , X ] = GibbsSamplerAT( WS , DS , AD , T , N , ALPHA , BETA , SEED , OUTPUT )
// Syntax
// [ WP , AT , Z , X ] = GibbsSamplerAT( WS , DS , AD , T , N , ALPHA , BETA , SEED , OUTPUT , ZIN , XIN )
// Updated for 64 bit compiler
int NAMAX ... |
a8ab1200f5c9cdd69793d51b1792407ea683299eb7dbdb52ff16284dccd1d80b | C++ | 15,599 | 446 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
0d42851fb20896ad2244b1d1b572a5a01fb7037558fb5369e8da684ee4d075ce | C++ | 15,638 | 446 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
4249a4910285ef087993aaa5055cb41eb5e7e434f61e4648069ac24d796b7f17 | C++ | 15,674 | 488 | #include "seprocessor.h"
#include "fastqreader.h"
#include <iostream>
#include <unistd.h>
#include <functional>
#include <thread>
#include <chrono>
#include <memory.h>
#include "util.h"
#include "jsonreporter.h"
#include "htmlreporter.h"
#include "adaptertrimmer.h"
#include "polyx.h"
SingleEndProcessor::SingleEndProce... |
cf556d01936a2a51da91604e7c7c1fcdb3de2c14913b80e8874947c3be559482 | C++ | 15,724 | 521 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
0846390d4e38659c75e60b137ad7a4afab962819949918035a0732a1641ce7c6 | C++ | 15,758 | 420 | /** @file layouts.cc
* @author David F. Gleich
* @date 2008-09-25
* @copyright Stanford University, 2008
* Graph layout wrappers
*/
/** History
* 2008-09-25: Initial coding
* 2008-09-27: Fixed progressive calls
*/
#include "include/matlab_bgl.h"
#include <yasmic/undir_simple_csr_matrix_as_graph.hpp>
#inclu... |
c3954a0b74b9bc22682541554e8b91608ffb8cb97ad2c95c115f146e95b89dbb | C++ | 15,894 | 415 | #include "lsl_c_api_helpers.hpp"
#include "stream_outlet_impl.h"
#include <loguru.hpp>
#pragma warning(disable : 4800)
extern "C" {
#include "api_types.hpp"
// include api_types before public API header
#include "../include/lsl/outlet.h"
using namespace lsl;
// boilerplate wrapper code
LIBLSL_C_API lsl_outlet lsl_c... |
a6a828f8b6b607b992e70a2aaddd1b7e09225acb7d9c58ecc60876762cc467fc | C++ | 15,903 | 521 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
0a35bd3ab0af0c71493c47288e5c9bc074676146034ae672adad14c76a32f667 | C++ | 15,935 | 449 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
3c83caa01481be1c86f2fddade24feef558f575958150bc758d8c47ed33b68f1 | C++ | 16,042 | 585 | //
// io_context.cpp
// ~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
... |
d9af72aa5a62fa49173bf30b02fdffabf5ee6f18203be8acf5313fe6fbfd4dc3 | C++ | 16,111 | 422 | #include "lsl_c_api_helpers.hpp"
#include "stream_outlet_impl.h"
#include <loguru.hpp>
#include <cstdint>
#include <exception>
#include <stdexcept>
#include <string>
#include <vector>
extern "C" {
#include "api_types.hpp"
// include api_types before public API header
#include "../include/lsl/outlet.h"
using namespace... |
34870849cd944a2f89d6f87564b5a1ec897af415121647c8276cd47d2b673603 | C++ | 16,260 | 494 | /**
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include "args.h"
#include <cstdlib>
#include <cstdint>
#include <iostream>
#include <stdexcept>
#include <str... |
4632a23cbb1610a19f9e7883de89d2bf34f7d99ef26ca3bd4cb65152a8d699e6 | C++ | 16,277 | 414 | //
// address_v6.cpp
// ~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
... |
2e38ad92980341af9bcccf48fb76a3bad6f2934a550f1e453ab9760140a9482e | C++ | 16,327 | 355 | #include "stitchWindowAligns.h"
#include "blocksOverlap.h"
#include "ErrorWarning.h"
#include "binarySearch2.h"
#include <cmath>
#include <ctime>
void stitchWindowAligns(uint iA, uint nA, int Score, bool WAincl[], uint tR2, uint tG2, Transcript trA, \
uint Lread, uiWA* WA, char* R, Genome &mapG... |
fa85b7106b2aa29d1de9d9d899078f701b8c18dbeb53456b8e8f1eb663e566c7 | C++ | 16,576 | 325 | #include "ReadAlign.h"
#include "GlobalVariables.h"
#include "ErrorWarning.h"
void ReadAlign::outputAlignments() {
outBAMbytes=0;
readAnnot.reset();
if (mapGen.pGe.gType==101) {//temporary
ReadAlign::spliceGraphWriteSAM();
return;
};
ReadAlign::outFilterBySJout... |
84174ba23a6b039f292daee7410b658f30808db4b83c277a7fdddd2a7a62544e | C++ | 16,703 | 594 | /*
* vbfa.cpp
* peer
*
* Created by Oliver Stegle on 11/12/10.
* Copyright 2010 __MyCompanyName__. All rights reserved.
*
*/
#include <iostream>
#include <assert.h>
#include "bayesnet.h"
#include <Eigen/Eigen>
#include <Eigen/Dense>
#include "vbfa.h"
#include "sparsefa.h"
#include "ossolog.h"
using namesp... |
69a3514b471b9579986ea94a0b146535e2e96af57d4f428e565c3caf96d0fedc | C++ | 16,728 | 449 | #include "mex.h"
#include "cokus.cpp"
// Syntax
// [ WP , DP , Z , X ] = GibbsSamplerSWBLDA( WS , DS , T , N , ALPHA , BETA0 , BETA1, BETA2 , GAMMA0, GAMMA1, GAMMA2, SEED , OUTPUT , ZIN , XIN )
// The Special Words plus Background (SWB) LDA model
void GibbsSampler( double ALPHA, double BETA0, double BETA... |
a0755dbae76dd56d119111b0ec4305b5e4eb70cb029c5e482a803e2389ee3c25 | C++ | 16,819 | 660 | /*
*
* Copyright (c) 1998-2002
* John Maddock
*
* Use, modification and distribution are subject to the
* Boost Software License, Version 1.0. (See accompanying file
* LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
*
*/
/*
* LOCATION: see http://www.boost.org for most recent versio... |
cc1d58aff1ab11aea6434996336c90ef610075575577cee33f26fb4901bcf017 | C++ | 16,925 | 472 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
//
// Eigen 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... |
a5b20f4c8fae53fd45144a6ef47155b37b1b3c9af975b1cafea5f974f3ad26c9 | C++ | 16,944 | 565 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
//------------------... |
e27fa250db9f3d0861323fde3f9faef50568f08e3022e941911f6a9b79ad7e44 | C++ | 16,952 | 629 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
b8f58083bf841865ef6225b5ca48509e984b60c1bcd2b9f92cb4669cab5c08da | C++ | 17,218 | 487 | /*
Copyright (c) Marshall Clow 2012.
Distributed under the Boost Software License, Version 1.0. (See accompanying
file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
For more information, see http://www.boost.org
*/
#include <boost/config.hpp>
#include <boost/algorithm/cxx11/copy_if.h... |
0c6b8889c8446a9dfe21ffc83aba942bacafdc135b800c6874d61cdf73bfbd06 | C++ | 17,358 | 498 | #define BOOST_MATH_DISABLE_STD_FPCLASSIFY
#include "sample.h"
#include "portable_archive/portable_iarchive.hpp"
#include "portable_archive/portable_oarchive.hpp"
#include "util/cast.hpp"
#include <boost/endian/conversion.hpp>
using namespace lsl;
using lslboost::endian::endian_reverse_inplace;
#ifdef _MSC_VER
#pragma... |
f1ac4f16710fe8828cc137566ce26e6a53f09918b0d16238006e6c132812a170 | C++ | 17,469 | 687 | #include "emitter.h"
#include "emitterstate.h"
#include "emitterutils.h"
#include "indentation.h"
#include "exceptions.h"
#include <sstream>
namespace YAML
{
Emitter::Emitter(): m_pState(new EmitterState)
{
}
Emitter::~Emitter()
{
}
const char *Emitter::c_str() const
{
return m_stream.str();
}
unsig... |
250c1c61a2fb9be783e5627cb4b4d776e264d754cde2cf869e46d0a579744a3a | C++ | 17,604 | 302 | #include "ReadAlignChunk.h"
#include "ThreadControl.h"
#include "ErrorWarning.h"
#include "SequenceFuns.h"
#include "GlobalVariables.h"
inline uint64 fastqReadOneLine(ifstream &streamIn, char *arrIn);
inline void removeStringEndControl(string &str);
void ReadAlignChunk::processChunks() {//read-map-write chunks
n... |
757c651eb4872e4eb5837240382d89870ed5bf4334cd0cf5361b5029f0c02603 | C++ | 17,631 | 733 | /* maxflow.cpp */
#include <stdio.h>
#include "graph.h"
/*
special constants for node->parent
*/
#define TERMINAL ( (arc *) 1 ) /* to terminal */
#define ORPHAN ( (arc *) 2 ) /* orphan */
#define INFINITE_D ((int)(((unsigned)-1)/2)) /* infinite distance to the terminal */
/*****************... |
10b881d98907b5296151105143844bdf7ebd8bd7aff860d19d36cbace15a75cb | C++ | 17,728 | 469 | #include "mex.h"
#include "cokus.cpp"
// Syntax
// [ WP,DP,WC,C,Z ] = GibbsSamplerLDACOL( WS , DS , SI , WW , T , N , ALPHA , BETA , GAMMA0, GAMMA1 , DELTA , SEED , OUTPUT );
// updated for 64 bit
void GibbsSamplerLDACOL( double ALPHA, double BETA, double GAMMA0, double GAMMA1, double DELTA, int W, int... |
334b7f16abc138b5faa07a7d9a8c9f631749bf39f22807bc7edc58843647d045 | C++ | 17,914 | 560 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
//------------------... |
6ec4deda480da6c209c32525700f02b4ad375db179b19c14c7ee349bd6a962b2 | C++ | 18,373 | 284 | // protect_test.cpp
//
// Copyright (c) 2009 Steven Watanabe
//
// Distributed under the Boost Software License, Version 1.0.
//
// See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#include <boost/bind/protect.hpp>
#include <boost/bind/bind.hpp>
#include <boost/core/lightweig... |
3d8fe6cf3685e25cc76c3dcfba12ed68ff2b5946bab22ddedc7996a077ba2124 | C++ | 18,425 | 438 | #include <cmath>
#include "Genome.h"
#include "IncludeDefine.h"
#include "Parameters.h"
#include "SuffixArrayFuns.h"
#include "PackedArray.h"
#include "TimeFunctions.h"
#include "ErrorWarning.h"
#include "GTF.h"
#include "SjdbClass.h"
#include "sjdbLoadFromFiles.h"
#include "sjdbPrepare.h"
#include "genomeParametersW... |
c379df30cabbc691cdcd565876a9a3508eec5f5db36dd72dde21310c4cefc9ef | C++ | 18,546 | 599 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// basic_archive.cpp:
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://... |
7fa473b91b86a1092b942eed68e6d408fe988a9005351a01e35b088bfa476508 | C++ | 18,634 | 429 | #include "SoloReadBarcode.h"
#include "serviceFuns.cpp"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
#include "GlobalVariables.h"
#include <chrono>
#include <thread>
void SoloReadBarcode::matchCBtoWL(string &cbSeq1, string &cbQual1, vector<uint64> &cbWL, int32 &cbMatch1, vector<uint64> &cbMatchInd1, string &cbM... |
7e13ecebb395786eefcb8828c3437ee9362055315a1a3e9ac23b672bf38e9de6 | C++ | 18,651 | 601 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// basic_archive.cpp:
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://... |
6fffe5af9879d16978a58fdae0a8a44891a26a51ec5ad5440aeee856f195c575 | C++ | 18,682 | 633 | #include "evaluator.h"
#include "fastqreader.h"
#include <map>
#include <memory.h>
#include "nucleotidetree.h"
#include "knownadapters.h"
Evaluator::Evaluator(Options* opt){
mOptions = opt;
}
Evaluator::~Evaluator(){
}
bool Evaluator::isTwoColorSystem() {
FastqReader reader(mOptions->in1);
Read* r = re... |
3896bd708ace0aa8d9984f044d5dfeaedeafe49c5e151c04f83d09cfff5bab53 | C++ | 18,776 | 474 | #include <stdlib.h>
#include "filterresult.h"
#include "stats.h"
#include "htmlreporter.h"
#include <memory.h>
#define MAX_ADAPTER_REC 20000
#define LOW_COMPLEXITY_SKIP 5000
FilterResult::FilterResult(Options* opt, bool paired){
mOptions = opt;
mPaired = paired;
mTrimmedAdapterRead = 0;
mTrimmedAdapte... |
7c58bd74511765c81ba51999f15b437f0f8eb198dc768d3f611156a5c19be229 | C++ | 18,819 | 568 | // SIMD-accelerated functions for fastp using Google Highway.
// This file is compiled once per SIMD target via foreach_target.h.
#undef HWY_TARGET_INCLUDE
#define HWY_TARGET_INCLUDE "src/simd.cpp"
#include <hwy/foreach_target.h> // IWYU pragma: keep
#include <hwy/highway.h>
HWY_BEFORE_NAMESPACE();
namespace fastp_s... |
2be4eeee971575aa7ce90a4fa4bf23a11e1cc2b5cf449913a343deb768bde3af | C++ | 19,029 | 706 | /***************************************************************************************************************
Copyright (c) 2011, Marco Reisert, Valerij G. Kiselev, Medical Physics, University Medical Center Freiburg
All rights reserved.
Reference: Reisert M, Mader I, Anastasopoulos C, Weigel M, Schnell... |
35b6402d30d706ec136377683794dc86c8cab5f5dbb55a5ad0d6ee372c70df34 | C++ | 19,156 | 778 |
#ifndef _PARTICLEGRID
#define _PARTICLEGRID
#include "auxilary_classes.cpp"
#include <list>
struct NeighborTracker // to run over the neighbors
{
int cellidx[8];
int cellidx_c[8];
int cellcnt;
int pcnt;
int gnum;
};
//////////////////////////////////////////////////////////////////////... |
14312eaf14499dab99901875450dde89a597502df8c57ae883d618fd370e4f44 | C++ | 19,392 | 658 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
220f8d5f838e738b987100e93dcee455f4548d5a5a5818054a117c8eb62cfb6b | C++ | 19,649 | 512 | /**
* @version pHARDI v0.3
* @copyright Copyright (C) 2017 Universidad Carlos III de Madrid. All rights reserved.
* @license GNU/GPL, see LICENSE.txt
* 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 Found... |
5f3f7b3a86aa4f035a76682eb9a619e4460638d5cb1f1111b48164c001fca12d | C++ | 19,740 | 528 | /**
* Copyright (c) 2017-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include <args.h>
#include <autotune.h>
#include <densematrix.h>
#include <fasttext.h>
#include <pybind11/numpy.... |
1ff140d7eadd4ce98c84de82e1241e9ad296f331e346e6079a71b3fc514a0d6c | C++ | 19,928 | 635 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
901e4bd0c0529214a00efad364dda0771429c116925ae7edf68e08996f316260 | C++ | 19,961 | 671 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
//
// Eigen 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 Soft... |
f1314d12aa51d03bb020dea42c32173e8985c734107ef958ceb729e306c6ecbb | C++ | 20,117 | 652 | /*
*
* Copyright (c) 2004
* John Maddock
*
* Use, modification and distribution are subject to the
* Boost Software License, Version 1.0. (See accompanying file
* LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
*
*/
/*
* LOCATION: see http://www.boost.org for most recent version.
... |
84e13de25e72c6d11c078afa3cee23088c1e19a10b546100f3da089ab29c40d2 | C++ | 20,131 | 617 | //---------------------------------------------------------------------------//
// Copyright (c) 2013 Kyle Lutz <kyle.r.lutz@gmail.com>
//
// Distributed under the Boost Software License, Version 1.0
// See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt
//
// See http://boostorg.gi... |
780433de2c8cde027ca02292c041473fc211a0f6309816d3be30f946de0a6e47 | C++ | 20,201 | 714 |
#include "ParticleGrid.cpp"
#include "EnergyComputerBase.cpp"
class EnergyComputer : public EnergyComputerBase
{
public:
REAL kappa;
REAL eigencon_energy;
REAL bound_attract;
REAL eigen_energy;
REAL ex_strength;
REAL in_strength;
REAL particle_length_sq;
REAL curv_hard;
REAL vf_smoot... |
49143254aaec68d218a1adfcbd96e85b0310a1dd5af838af700a6f4bf25ec998 | C++ | 20,251 | 655 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
#include "snippets.h... |
dfa205a7d8cdfb80c4459aa3e37e67058e1d41f58812e90e0826af954a338ff3 | C++ | 20,305 | 563 | #include "mex.h"
#include "cokus.cpp"
// Syntax
// [ WP , DP , MP , Z , X ] = GibbsSamplerHMMLDA( WS , DS , T , S , N , ALPHA , BETA , GAMMA , SEED , OUTPUT )
// Syntax
// [ WP , DP , MP , Z , X ] = GibbsSamplerHMMLDA( WS , DS , T , S , N , ALPHA , BETA , GAMMA , SEED , OUTPUT , ZIN , XIN )
// updated f... |
214ac3c3865423834ff11eb5806b2a9470b0ddff3d8dd9e5e431da46087e4588 | C++ | 20,455 | 742 | // Demonstration of rules when an iterator is considered to be valid if the soft
// iterator invalidation definition is applied.
// Note: The soft iterator invalidation definition CAN NOT be applied
// to the space optimized circular buffer.
// Copyright (c) 2003-2008 Jan Gaspar
// Use, modification, and distri... |
13bedd9be19f3335f2c651c46cf88c8e8b438f3c393f1f0dfc9125f400465f44 | C++ | 20,534 | 489 | #include "mex.h"
#include "cokus.cpp"
// Syntax 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
// [ DP_NEW,C,Z,PROB ] = NewDocumentsLDACOL( WS_NEW , DS_NEW , SI_NEW , W... |
c15b228299d8042813d9aac1246b2619204b3c19ac2ece7216a2fc9ad6465b96 | C++ | 20,657 | 712 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
//------------------... |
84d31fff54c1d5a3b8eda85f0d1abdd49227536b58e371d1e8146f526913fc5d | C++ | 20,675 | 415 | #include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "extendAlign.h"
#include "binarySearch2.h"
// #include "stitchGapIndel.cpp"
intScore stitchAlignToTranscript(uint rAend, uint gAend, uint rBstart, uint gBstart, uint L, uint iFragB, uint sjAB, Parameters& P, char* R, Genome &mapGen, T... |
d2e19d96f2ac7186f8afd35129bda0b2c49b585e0674997b35358cdcba753667 | C++ | 20,701 | 582 | /** @file planar.cc
* @author David F. Gleich
* @date 2008-09-29
* @copyright Stanford University, 2008
* Planar graph algorithm wrappers
*/
/** History
* 2008-09-29: Initial coding
*/
#include "include/matlab_bgl.h"
#include <yasmic/undir_simple_csr_matrix_as_graph.hpp>
#include <yasmic/simple_csr_matrix_as... |
3d2e7c3621f4e77bae88080924e605adc1dc2e3499d177fa42400527be18c836 | C++ | 20,744 | 700 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
//------------------... |
21d63120ad76af36951dc2a4660bfd0d97791caaef13ace7df488af1bf5df9b4 | C++ | 20,901 | 413 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
5243d9b59bb2dc9149b1146b44ba36bd6ecee2ac31d1d122f24092c02f5dba77 | C++ | 20,905 | 597 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
9758de865c2b18c5bf2c93c04d78df52208f6ba472f9a3aa8cbbf06fef1576f1 | C++ | 20,981 | 503 | #include <mex.h>
#include <stdio.h>
#include <map>
#include <string>
#include "../GCoptimization.h"
#if !defined(MX_API_VER) || MX_API_VER < 0x07030000
typedef int mwSize;
typedef int mwIndex;
#endif
// MATLAB 2014a: mxCreateReference is NO LONGER AVAILABLE :(
//extern "C" mxArray *mxCreateReference(const... |
00281db7388b3287f507c4e1e3111b738820cd5ee4bf836ba8bc2810d2d5b2fd | C++ | 21,136 | 715 |
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header fi... |
308b78c8b8a33725bbc231c00c45e74e61234bbfc4c6adff39fb27bb0baebe9c | C++ | 21,192 | 577 | //
// icmp.cpp
// ~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#if !defined... |
89d832742e39eda6e55135c4c54fe0651dbdaed22611646b3055e83e1403ebd6 | C++ | 21,205 | 525 | #include "options.h"
#include "util.h"
#include <iostream>
#include <fstream>
#include <string.h>
#include "fastareader.h"
#include <thread>
Options::Options(){
in1 = "";
in2 = "";
out1 = "";
out2 = "";
reportTitle = "fastp report";
thread = 3;
compression = 4;
phred64 = false;
dont... |
233ad9214de411003ebb8cd4f703d29b501ee1fef2065ca059b37eb6911dcb6d | C++ | 21,256 | 660 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
7a8d873b6657bd28e7826411671513141a5051f1694ed6105e7299d2d66b95db | C++ | 21,354 | 656 | #include<stdio.h>
#include<string>
#include<stdlib.h>
#include<math.h>
#include <sys/time.h>
using namespace std;
# define gr (double)1.0
void sol_0(double t0, double t, double *x0, double *x, double *para, double *para2);
void sol_1(double t0, double t, double *x0, double *x, double *para, double *para2);
void com... |
7e211bbc161b1d29e3ac444a66f968a8cc787e227ceec5b947a7a05e8bfd635f | C++ | 21,409 | 511 | /*
*
* Copyright (c) 2004
* John Maddock
*
* Use, modification and distribution are subject to the
* Boost Software License, Version 1.0. (See accompanying file
* LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
*
*/
/*
* LOCATION: see http://www.boost.org for most recent version.
... |
705114394f846f5fab95398f12363b2679ca1f675b6c329ce32f34963ace0c1d | C++ | 21,720 | 928 | /*
*
* Copyright (c) 1998-2002
* John Maddock
*
* Use, modification and distribution are subject to the
* Boost Software License, Version 1.0. (See accompanying file
* LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
*
*/
/*
* LOCATION: see http://www.boost.org for most recent versi... |
8c91c44dfbd75110595e871ddd6cb6d4f885a20136a427a68d6b9fa0734776e0 | C++ | 22,545 | 754 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
c58d7774794ce54cfcd0f4bd40fb31bb87b7a8a2f39be49a354f9611175a016a | C++ | 22,991 | 578 | #include "tcp_server.h"
#include "api_config.h"
#include "cast.h"
#include "consumer_queue.h"
#include "sample.h"
#include "send_buffer.h"
#include "socket_utils.h"
#include "stream_info_impl.h"
#include <boost/asio/io_context.hpp>
#include <boost/asio/ip/host_name.hpp>
#include <boost/asio/ip/tcp.hpp>
#include <boost/... |
e77f55f86d028b147315f32f49f6934907bd5c9459fdc3418a2a239f7caaac99 | C++ | 23,055 | 759 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
f6a85ef14d13e814d3291ee86ce17599590fb778f65268bbe2eafdf37bc77542 | C++ | 23,528 | 521 | #include "Genome.h"
#include "SuffixArrayFuns.h"
#include "PackedArray.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include "SharedMemory.h"
#include "genomeScanFastaFiles.h"
//addresses with respect to shmStart of several genome values
#define SHM_sizeG 0
#define SHM_sizeSA 8
#define SHM_startG 16
// #define... |
dc334df19719b9c898c63d2e6b7f85c40f2d4764d16e2532447a22fd66c85c9e | C++ | 23,759 | 615 | #include "tcp_server.h"
#include "api_config.h"
#include "consumer_queue.h"
#include "sample.h"
#include "send_buffer.h"
#include "socket_utils.h"
#include "stream_info_impl.h"
#include "util/cast.hpp"
#include "util/endian.hpp"
#include "util/strfuns.hpp"
#include <asio/io_context.hpp>
#include <asio/ip/host_name.hpp>... |
fe6e14ea86c6413b09c90fb43bb99d0cc222f1590478d5834720790197812092 | C++ | 23,773 | 988 | #include "tests.h"
#include "yaml.h"
#include <sstream>
#include <algorithm>
namespace Test
{
namespace Parser {
void SimpleScalar(std::string& inputScalar, std::string& desiredOutput)
{
inputScalar = "Hello, World!";
desiredOutput = "Hello, World!";
}
void MultiLineScalar(std::string& inputScalar, std... |
3a62cfcfbb58026d1e318aa9cc84520cdf247355079b18049278bd207ca0bc16 | C++ | 23,850 | 667 | #include "bgmg_parse.h"
#include <algorithm>
#include <sstream>
#include <fstream>
#include <boost/algorithm/string.hpp>
#include "bgmg_log.h"
#include "bgmg_serialize.h"
#include "zstr.hpp"
// Validate that all characters are A, T, C, G - nothing else. Expect lower case allele codes.
static bool check_atcg(std::s... |
44fe661137e8219036c30596887f331d9cc9ccc41fed0857e23aac864b342602 | C++ | 23,912 | 673 | //
// udp.cpp
// ~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#if !defined(B... |
5368996d5c508c5301bf588e24d4ae5c94b6571efc082c05ef65356e39689095 | C++ | 23,953 | 823 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
118e63a77e7ea2febe75185fa880defc208678991a34b9c979cdccf6e5623b4d | C++ | 24,040 | 629 | #include "htmlreporter.h"
#include <chrono>
#include <memory.h>
#include "knownadapters.h"
extern string command;
HtmlReporter::HtmlReporter(Options* opt){
mOptions = opt;
mDupHist = NULL;
mDupRate = 0.0;
}
HtmlReporter::~HtmlReporter(){
}
void HtmlReporter::setDup(double dupRate) {
mDupRate = dupRa... |
fc75a0ddeb42ce0b369a1ee45bbbc10a4fd07ca2ca491e3c8d120329ce928428 | C++ | 24,118 | 690 | // 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 ... |
36e909dfb0bfecddd556d14df7995ce107a335f2cca2d78975da238b3eca3561 | C++ | 24,123 | 713 | // 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 ... |
cd52e814bd760f83cfe0adc1b55ba270a51cf7bdcd41e810e20c4ab34e1b5a28 | C++ | 24,159 | 844 | //
// set_value.cpp
// ~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#i... |
6ae8863af71aa957e0912d60f66490336566de62102485a01b7c1d63e2504821 | C++ | 24,459 | 767 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
07292cbcec567a10193e8ef2bca265fab6985025bdcfc899c807c98aeb4e4855 | C++ | 24,481 | 832 | /**
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include "fasttext.h"
#include "loss.h"
#include "quantmatrix.h"
#include <algorithm>
#include <iomanip>
#inclu... |
51b40f71754b165f35cd65431adae656d01e923b9333e9f2b119e39773deb991 | C++ | 24,972 | 650 | //
// socket_base.cpp
// ~~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests... |
fde508940e0678a7177572025e5b0974af6a412ed68f553373e330af19018bb0 | C++ | 25,061 | 639 |
/*
LICENCE
The Software remains the property of the University Medical Center
Freiburg ("the University").
The Software is distributed "AS IS" under this Licence solely for
non-commercial use in the hope that it will be useful, but in order
that the University as a charitable foundat... |
1b346abce52cab7e31f9443ae2601b747d4365d0f0dbf1ffc0d648ed2995b0b6 | C++ | 25,695 | 866 | // Test of the base circular buffer container.
// Copyright (c) 2003-2008 Jan Gaspar
// Copyright (c) 2013 Antony Polukhin
// Use, modification, and distribution is subject to the Boost Software
// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
#inclu... |
e392b14465b21218ea6b33492f817a6ef2cdbdfdbeb5b05056559e3494b1e41d | C++ | 25,778 | 796 | // Copyright (C) 2001-2003
// William E. Kempf
// Copyright (C) 2007-8 Anthony Williams
// (C) Copyright 2011-2012 Vicente J. Botet Escriba
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
#include <boost/threa... |
a087853ada319b507200101dde0524e3df6fb476cfa652ce130caccfe981c17d | C++ | 26,189 | 479 | /**
* @license
* Copyright 2016 Google Inc.
* 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
*
* Unless required by applicable law or... |
793fab6d8619313d395101f3fe2ae9d0ce9695622d56ee3889dc6a3676c0d27c | C++ | 26,911 | 856 |
#include "ParticleGrid.cpp"
#include "RJMCMCBase.cpp"
#include <list>
class RJMCMC : public RJMCMCBase
{
public:
REAL Temp;
REAL expected_nump;
REAL Vol;
REAL sigma_g;
REAL sigma_g_dir;
REAL dthres;
REAL nthres;
REAL T_prop;
REAL len_def;
REAL maxD;
REAL bias;
REAL modelp... |
f68170bda616fbfe08bc6fdcab0597987178b979e0cc1853b06cbefc709ba095 | C++ | 27,376 | 830 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
d55cad3ffc7a6d6101bf87aa1f289b692bed99a9875a14f21f8cc3cbd36c5ed5 | C++ | 27,549 | 888 | //
// any_executor.cpp
// ~~~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tes... |
10aa94a3694a574efbb7c2aa27db7640059bfc6cb172018184f4f60ae9d8e515 | C++ | 27,565 | 819 | /** @file statistics.cc
* @author David F. Gleich
* @date 2006-04-21
* @copyright Stanford University, 2006-2008
* Graph statistics wrappers
*/
/** History
* 2007-04-18: Implemented topological order function
* 2007-07-05: Implemented matchings
* 2007-07-05: Implemented core_numbers
* 2007-07-11: Implemen... |
65c2db01050bde76fe29b74428272cd5e847406f687712328599996421aab0f7 | C++ | 27,711 | 860 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
// Test that header ... |
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