sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8013ee68d61c181e4e936cdae3a9a635646274f8512033ef11bff7214e03e4a6 | C++ | 5,099 | 130 | // 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... |
8c2cd6aa503d091766c902b4847ade1f301b0e6fde75cc1c638854f76d340697 | C++ | 5,101 | 187 |
//g++ -O3 -g0 -DNDEBUG sparse_product.cpp -I.. -I/home/gael/Coding/LinearAlgebra/mtl4/ -DDENSITY=0.005 -DSIZE=10000 && ./a.out
//g++ -O3 -g0 -DNDEBUG sparse_product.cpp -I.. -I/home/gael/Coding/LinearAlgebra/mtl4/ -DDENSITY=0.05 -DSIZE=2000 && ./a.out
// -DNOGMM -DNOMTL -DCSPARSE
// -I /home/gael/Coding/LinearAlgebr... |
8ebb9b3d521cc3392953f27658cf1f6dcb763216079f69a1518ec5ca0e42a63b | C++ | 5,112 | 329 |
#include "zfstream.h"
gzfilebuf::gzfilebuf() :
file(NULL),
mode(0),
own_file_descriptor(0)
{ }
gzfilebuf::~gzfilebuf() {
sync();
if ( own_file_descriptor )
close();
}
gzfilebuf *gzfilebuf::open( const char *name,
int io_mode ) {
if ( is_open() )
return NULL;
cha... |
1f1588fdf2df3b2133cbc20abab5e25e023b05a9b542abda73f7e6ca038ce780 | C++ | 5,116 | 166 | //
// random_access_handle.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 autolink... |
8016fffeb6e9828f3c23ce157acac28ea09ab071e39443dbea56b8a247b5aa78 | C++ | 5,122 | 158 | // Boost string_algo library substr_test.cpp file ------------------//
// Copyright Pavol Droba 2002-2003. 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)
// See http://www... |
d15192bd9187c7f651d83572afc8dc30337f5f2ab7ad5b63dbc6dd632f900b71 | C++ | 5,124 | 141 | // 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... |
43a7a08452fb4331014f1f144f9b637f576e8b73994f1825b7e9698cbee75467 | C++ | 5,131 | 129 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2007-2010 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Publ... |
7350918a663691aaf2c7b2edeef686d1f418962a7f3a97b075749bcde7843197 | C++ | 5,132 | 169 | // Copyright 2001, 2002, 2020 Peter Dimov
// Distributed under the Boost Software License, Version 1.0.
// https://www.boost.org/LICENSE_1_0.txt)
#include <boost/mem_fn.hpp>
#include <boost/shared_ptr.hpp>
#include <iostream>
#if defined(BOOST_NO_CXX11_NOEXCEPT)
int main()
{
}
#else
struct X
{
mutable unsigned... |
904be0d4a095e74393515195392bd10e1e916bb2ca61f3f94b1bd6aebea29cb6 | C++ | 5,132 | 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 ... |
3871b516c23e0618b65c390d74f84a2a692b2265e45ae49b32a3c2a539ff9391 | C++ | 5,137 | 175 | // Boost.Bimap
//
// Copyright (c) 2006-2007 Matias Capeletto
//
// 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)
// VC++ 8.0 warns on usage of certain Standard Library and API functions that
// can be cause bu... |
d4952d9200d6c7216d5e7c1212b8af38923f5264c22882e80730fc1554bd980a | C++ | 5,146 | 109 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// 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 Softwar... |
35515298827106944a813746e0ee2e3d481f1eec1049bcb8043ccc0802f5bb44 | C++ | 5,162 | 103 | /*
Copyright Barrett Adair 2016-2017
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE.md or copy at http ://boost.org/LICENSE_1_0.txt)
*/
#include <type_traits>
#include <functional>
#include <tuple>
#include <boost/callable_traits/add_member_const.hpp>
#include "test.hpp"
str... |
7c4b8dbd4a7991860029f2c4ab04a089dc428a3136a576a32dc07af093df8970 | C++ | 5,182 | 177 | //
// serial_port.cpp
// ~~~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
// Copyright (c) 2008 Rep Invariant Systems, Inc. (info@repinvariant.com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http:... |
e85f2417ca0d41bb0fdb3a59e1e4b21e7e382f217757a01ef1224cca66cc40bd | C++ | 5,193 | 135 |
#include <iostream>
#include <Eigen/Core>
#include <bench/BenchTimer.h>
using namespace Eigen;
#ifndef SIZE
#define SIZE 50
#endif
#ifndef REPEAT
#define REPEAT 10000
#endif
typedef float Scalar;
__attribute__ ((noinline)) void benchVec(Scalar* a, Scalar* b, Scalar* c, int size);
__attribute__ ((noinline)) void be... |
88873afff744c176dd46ccd2c0fb224b97352de294f715b94c0ec5907a7779b9 | C++ | 5,202 | 136 | /*
Copyright (c) Marshall Clow 2011-2012.
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 <iostream>
#include <boost/config.hpp>
#include <boost... |
82b0e2fc86b87adeac47a2b474b81a6238aa9cfd899a1813f6c633c5944295e8 | C++ | 5,212 | 125 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 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 Soft... |
9a868132fa48a3b9dda5e79a802abd8d6c80430b27c33e1531d26fcb1a7823cc | C++ | 5,213 | 111 | #include "Parameters.h"
#include "ErrorWarning.h"
#include <fstream>
#include <sys/stat.h>
void Parameters::openReadsFiles()
{
if (readFilesCommandString=="") {//read from file
for (uint ii=0;ii<readFilesIn.size();ii++) {//open readIn files
readFilesCommandPID[ii]=0;//no command process IDs
... |
3936d3e8f80fdc4f6a3550e18588d3bcc82dcca398fea7d9ae8f90c53d14612f | C++ | 5,214 | 184 | //
// 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 ... |
e3bad52ba2869439228af72078781495e2386a3731ef580b4c1bcc70a763d1d7 | C++ | 5,216 | 160 | //---------------------------------------------------------------------------//
// Copyright (c) 2013-2014 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://boosto... |
f2ff02da129dcd05c705a2216c1e4c25a4d1481a702feebb02946daa8f44eb50 | C++ | 5,216 | 236 | //
// start.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 !defin... |
5792cd05899f231d1318682eee5a18799ff0030b83c1992bdd3b01e99821f817 | C++ | 5,230 | 162 | // Boost string_algo library find_format_test.cpp file ------------------//
// 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)
// See http://www.boost.org for updates, ... |
482b518839e198920d5af92c0356827ea527b793f934f3b05351945b70c8457b | C++ | 5,243 | 169 | #include "duplicate.h"
#include "overlapanalysis.h"
#include <memory.h>
#include <math.h>
#include "util.h"
const int PRIME_ARRAY_LEN = 1<<9;
Duplicate::Duplicate(Options* opt) {
mOptions = opt;
// 1G mem required
mBufLenInBytes = 1L <<29;
mBufNum = 2;
// the memory usage increases as the accura... |
91cce24f031b42a6d0d765ee9691d7fb3bf1e936bd59f17c0e65edf40e4ec42c | C++ | 5,248 | 163 | // 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 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
//... |
0209f221f1e7e5614cff859f4f50e16c5ae214e35d41de0583fe2aa5ca44d90c | C++ | 5,252 | 147 | //---------------------------------------------------------------------------//
// 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... |
28fccbe8df679125525a783b8e84352d5e4e3edc73fa33bc0c352a07683775aa | C++ | 5,255 | 118 | #include "ReadAlign.h"
#include "SequenceFuns.h"
#include "Stats.h"
#include "serviceFuns.cpp"
int ReadAlign::mapOneRead() {
#ifdef OFF_BEFORE_SEEDING
#warning OFF_BEFORE_SEEDING
nW=0;
return 0;
#endif
revertStrand = false; //the 2nd read is awlays on opposite strand. 1st and 2nd ... |
22715bd2b3fe879ed4574b708dd43b2dafa55ca11e579016abcee4aab3c858f3 | C++ | 5,260 | 167 | //---------------------------------------------------------------------------//
// 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... |
559c8754355357f98666b6373366b24160c70a1ab1ddda3717bf568576d8ce3e | C++ | 5,265 | 181 | //
// stream_file.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... |
4369bdc5a406196f539b6ae6f82165085c19490d3a1b6a670eaa6e81ed4eef7a | C++ | 5,267 | 162 | //---------------------------------------------------------------------------//
// Copyright (c) 2013-2014 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://boosto... |
0deb0526f49394d92d2be22857a7c7a0632129f066fdaadcc621343996570e5b | C++ | 5,274 | 114 | #include "Transcriptome.h"
#include "ReadAlign.h"
#include "serviceFuns.cpp"
int alignToTranscript(Transcript &aG, uint trS1, uint8 trStr1, uint32 *exSE1, uint32 *exLenCum1, uint16 exN1, Transcript &aT) {
//find exon that overlaps beginning of the read
uint32 g1=aG.exons[0][EX_G]-trS1;//start of the align
... |
2826480d31c7bf6a8bbc6bfc4930e1c1e3049eeb123e81282101f6885ad1b9a9 | C++ | 5,286 | 132 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// 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 Softwar... |
f6bc7be0b8e4824473f8752cd11b12d12a76f0cb5dbb00ae3de9f3bec831407b | C++ | 5,290 | 160 | // Boost string_algo library predicate_test.cpp file ------------------//
// Copyright Pavol Droba 2002-2003. 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)
// See http://... |
61f85fad5da520266e844406f91f5bcafb4b9d24dddd8a65314300200793f513 | C++ | 5,294 | 129 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2007-2010 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Publ... |
96a6a1ca0fa56b63e5eeb0d1f38311b52d748c0021c386aded65e087f51b1f07 | C++ | 5,297 | 130 | #include "IncludeDefine.h"
#include "Parameters.h"
#include "ReadAlign.h"
#include "ErrorWarning.h"
void ReadAlign::assignAlignToWindow(uint a1, uint aLength, uint aStr, uint aNrep, uint aFrag, uint aRstart, bool aAnchor, uint sjA) {
uint iW=winBin[aStr][a1>>P.winBinNbits];
if (iW==uintWinBinMax || (!aAnchor... |
efcef3ee5b89490bf1d235085d2cc7ff6616cdd8ddf6b48d851600522e0ecf8d | C++ | 5,304 | 193 | // Test of the space optimized adaptor of the circular buffer.
// Copyright (c) 2003-2008 Jan Gaspar
// 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)
#include "test.hpp"
#define... |
9e14e78958efe0019bbafb6a29b746d449cd4b7544db94b37151d87f8cd186e6 | C++ | 5,311 | 156 | // miscellaneous.cpp ----------------------------------------------------------//
// Copyright 2008 Howard Hinnant
// Copyright 2008 Beman Dawes
// Copyright 2009 Vicente J. Botet Escriba
// Distributed under the Boost Software License, Version 1.0.
// See http://www.boost.org/LICENSE_1_0.txt
/*
This code was... |
736d3d4517abef65dcc8b15b6490ee92acd7d72f873a1a03077e7b3c3ea06de6 | C++ | 5,317 | 106 | /*
Copyright Barrett Adair 2016-2017
Distributed under the Boost Software License, Version 1.0.
(See accompanying file LICENSE.md or copy at http ://boost.org/LICENSE_1_0.txt)
*/
#include <type_traits>
#include <functional>
#include <tuple>
#include <boost/callable_traits/remove_member_const.hpp>
#include "test.hpp"
... |
89895129b11486b22ea26292ba009ef60a48bd05aa151a011d45e1bd6beda190 | C++ | 5,326 | 102 | //---------------------------------------------------------------------------//
// 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... |
0cf4a0fb2780f3a5e9a7e6fe5271849ff8fb53a28e4802a0df8ffeb7abf422e0 | C++ | 5,348 | 184 | #include <boost/config.hpp>
#if defined(BOOST_MSVC)
#pragma warning(disable: 4786) // identifier truncated in debug info
#pragma warning(disable: 4710) // function not inlined
#pragma warning(disable: 4711) // function selected for automatic inline expansion
#pragma warning(disable: 4514) // unreferenced inline re... |
252c06b4531dc35213ebdd7311700b9b4057bc1bdeeba0cd767b2bc86c456639 | C++ | 5,351 | 151 | // 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 ... |
5c856902c0011b48150ffe5631b662b551e2f3e2a1c9c934180665fe78ddb142 | C++ | 5,356 | 113 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2006-2010 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// 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 So... |
74539a4abff06d28660a179467ec5958fb652d10c179069380b8ac41849c8d08 | C++ | 5,357 | 111 | // 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... |
07e1c44ddc06fd1c048207cb2d9725459355976a2603343a7c139bd63ecd832d | C++ | 5,363 | 164 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// 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 Softwar... |
4a5ad2c0066acd34f34350fb74dfcfa4b83b6b86cbcc7b1aea4dc3ec94fd4c6f | C++ | 5,367 | 188 | #include "scanscalar.h"
#include "scanner.h"
#include "exp.h"
#include "exceptions.h"
#include "token.h"
namespace YAML
{
// ScanScalar
// . This is where the scalar magic happens.
//
// . We do the scanning in three phases:
// 1. Scan until newline
// 2. Eat newline
// 3. Scan leading blanks.
//
// . D... |
12d46f39ff22e1a1cc9d5ee169946b1bf433827494b9aef8edfaf36451d07c60 | C++ | 5,373 | 118 | #include "ParametersChimeric.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "GlobalVariables.h"
void ParametersChimeric::initialize(Parameters *pPin)
{
out.bam=false;
out.junctions=false;
out.samOld=false;
out.bamHardClip=true;//default
if (segmentMin==0)
return;
... |
a32b1b45b7bedeb7a7991d6e825139652975ec28003f794191b5259584a3f792 | C++ | 5,379 | 163 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// 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 Softwar... |
1539d2e8e288b16c8dad7ae30c975fbddf697779f0fda80609ca4ab32850b273 | C++ | 5,380 | 108 | // 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... |
149f0c1bfa3c9cc7afcb936773e215fcf2d703518e32326d2b76f316be56a563 | C++ | 5,382 | 156 | // thread_primitives.cpp
//
// (C) Copyright 2018 Andrey Semashev
//
// 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/winapi/config.hpp>
#include <boost/winapi/dll.hpp>
#include <boost/winapi... |
062dd189ec498e30febf4dba5c6183e413196a2615d9bdaf0080ccf847625a11 | C++ | 5,387 | 174 | // (C) Copyright Eric Niebler 2005.
// 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)
// Test case for extended_p_square_quantile.hpp
#include <iostream>
#include <boost/random... |
212e8c17160cc8aa2de624babb7f4c700a57fe2692f91be88d364bd4ba87e150 | C++ | 5,392 | 163 | // 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 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
//... |
7baabc3f5519451829a305e528fb4ae8e0582ff6bc97f979623bcf831e52e87d | C++ | 5,393 | 218 | #include <boost/config.hpp>
#if defined(BOOST_MSVC)
#pragma warning(disable: 4786) // identifier truncated in debug info
#pragma warning(disable: 4710) // function not inlined
#pragma warning(disable: 4711) // function selected for automatic inline expansion
#pragma warning(disable: 4514) // unreferenced inline re... |
7a2714443408e99015fa5ba454e115dcafad15584213545d0bbf9d9ba5334381 | C++ | 5,402 | 164 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// 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 Softwar... |
c35e8219ec59a6da9ac926ecc244fc3849d25dfaf4d44c3218c103dcb2002ec1 | C++ | 5,408 | 198 | // Boost.Bimap
//
// Copyright (c) 2006-2007 Matias Capeletto
//
// 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)
// VC++ 8.0 warns on usage of certain Standard Library and API functions that
// can be cause bu... |
3d0179e2bfc35931f1fdd0ceb0ccfd8df49184bc3c8027decf5d81b9d1e08f8c | C++ | 5,413 | 187 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 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
// License as published by the Free Software Found... |
329b9b54ad1fd1edc5334f336d83509c79e26ff122a8169d9d09a0f8a1399182 | C++ | 5,415 | 173 | // 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>
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify... |
ae5e694a3ca25db4ecd8776f1304351d325b50e47186c08f5a9f45ef7514f0a8 | C++ | 5,419 | 113 | // 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... |
11349052c8c4617e8145b05e85701cf536ca455e296ac2a4764b705855bc7a26 | C++ | 5,422 | 173 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU ... |
9c9fd8f5d85edfd25a26d95cf24e9f079cdd5aaaf03b4610c83feaa06ccf63e9 | C++ | 5,425 | 170 | //
// system_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 un... |
e908ffb5a3a4136e974febce2386688e503ce6d3f0bf054210f271423c25a085 | C++ | 5,429 | 236 | //
// set_done.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 ... |
6e886600670b88b7aa85e87eb5804e6865c7f1b30867e429a823892afe59ddc9 | C++ | 5,440 | 225 | //
// bind_cancellation_slot.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 auto... |
00fcf15740bc89c28fb75420278b1a68670b2572f8cf57e361f8d5b1f8863255 | C++ | 5,441 | 229 | // Guy Shechter
// June 2004
// ********
// Edit kdtree_common.h to set architecture specific pathnames.
// ********
//
// You can turn on some of the following definitions to debug this file.
//
#undef DEBUG //General input-output debugging information
#undef DEBUG_BUILD_TREE //Follow how the k-D tree is... |
2345a121ca342d05d152c8de60496fb87015996916be21d4a8a8105b00dc5492 | C++ | 5,450 | 140 | // cycle_count.cpp ----------------------------------------------------------//
// Copyright 2008 Howard Hinnant
// Copyright 2008 Beman Dawes
// Copyright 2009 Vicente J. Botet Escriba
// Distributed under the Boost Software License, Version 1.0.
// See http://www.boost.org/LICENSE_1_0.txt
/*
This code was e... |
98cbb210f4b59020821555d47c147bb430fcb38bb47a556c5377bd9b461175fb | C++ | 5,455 | 127 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2010 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... |
39329a62ccd45e5034ea9320c6a0272d0b49dfbb7312d6b97b4b0b6fe718d3d5 | C++ | 5,456 | 173 | // 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>
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify... |
076d74764691a18af95b53b9388a677be9b2b3acfb3ad9edfb06d2ffcf894f9a | C++ | 5,462 | 105 | #include "ChimericAlign.h"
#include "ReadAlign.h"
#include "BAMfunctions.h"
#include <vector>
void ChimericAlign::chimericBAMoutput(Transcript *al1, Transcript *al2, ReadAlign *RA, const uint iTr, const uint chimN, const bool isBestChimAlign, const Parameters& P)
{
vector<Transcript*> trChim(2);
trChim[0] = a... |
816f89467516608d32223d1002e3be8be5c5a216f94a63153b3a39721c30c69b | C++ | 5,466 | 189 | //
// 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
//
//------------------... |
0a8229fcd507f8639941484a410ebc01cd25b46b1c95918fe2ca455de2d6dcd7 | C++ | 5,472 | 164 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Jitse Niesen <jitse@maths.leeds.ac.uk>
//
// 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 Software... |
952032d4c35ffd907271f2f885f0a2f49d4d87f575621024e790fa9c0e7be0bd | C++ | 5,483 | 237 | // Guy Shechter
// June 2004
// ********
// Edit kdtree_common.h to set architecture specific pathnames.
// ********
//
// You can turn on some of the following definitions to debug this file.
//
#undef DEBUG //General input-output debugging information
#undef DEBUG_BUILD_TREE //Follow how the k-D tree i... |
05816fe30a14b4a219b9f03f9ea434972bd9d64c660fd30df3ca17b5f08aa91f | C++ | 5,486 | 238 | #include "map.h"
#include "node.h"
#include "scanner.h"
#include "token.h"
#include "exceptions.h"
#include "emitter.h"
namespace YAML
{
Map::Map()
{
}
Map::Map(const node_map& data)
{
for(node_map::const_iterator it=data.begin();it!=data.end();++it) {
std::auto_ptr<Node> pKey = it->first->Clone();
std:... |
885b67ce03753a0d3ea8d2a11998532d1c0e97e48aa460bc0d400ea3e73be297 | C++ | 5,494 | 186 | /*
==============================================================================
SpikeBandMedianSubtraction
(c) 2017 Allen Institute for Brain Science
written by joshs@alleninstitute.org
==============================================================================
*/
// VERSION 0.1 //
... |
b1fc68f8b75ce25fbd79b3f7d3c9c793381ef07b3203e1a2d9b610cb597542be | C++ | 5,497 | 166 | // 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 ... |
6d75d76961bf51ddf1e633db0f54200c0a82b6ddaa17ec527c2d249e52931b48 | C++ | 5,500 | 149 | // boost win32_test.cpp -----------------------------------------------------//
// Copyright 2010 Vicente J. Botet Escriba
// Distributed under the Boost Software License, Version 1.0.
// See http://www.boost.org/LICENSE_1_0.txt
// See http://www.boost.org/libs/chrono for documentation.
#include <boost/chrono/... |
685cfff006c375b327c5f1c6160e1e5f9d4849c7270bd887ddc75efe5c3bf164 | C++ | 5,515 | 199 | //
// 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 ... |
732adc864da78b6a46518fc3241e7fef89b869491580511154be2da57e8b846e | C++ | 5,515 | 179 | //
// random_access_file.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 ... |
ca59ff54a49da94444d41d4595f6fd33bb6433ca1613803c5f021a345d90c8e1 | C++ | 5,517 | 107 | #include "ParametersClip.h"
#include "Parameters.h"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
void ParametersClip::initialize(Parameters *pPin)
{
pP = pPin;
//yes = false;
if (adapterType[0]!="Hamming" && adapterType[0]!="CellRanger4") {
exitWithError("EXITING because of fatal PARAME... |
0e88275f5e9901e372493a35aad8395d9ca18f1c7d977de69f13fd7c105b7e61 | C++ | 5,519 | 226 | //
// request_parser.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)
//
#include "request_parser.hpp"
#... |
a03337eaa8d42c8dbf6668f2d7d82b411efce20a252f1aa26690c72c1c046ef7 | C++ | 5,519 | 160 | /***************************************************************************************************************
Copyright (c) 2011, Marco Reisert, Valerij G. Kiselev, Medical Physics, University Medical Center Freiburg
All rights reserved.
Redistribution and use in source and binary forms, with or without... |
5a2a5054f21481e172d8071993f720d97e4b1da14315edc695fa7642902d2ddc | C++ | 5,521 | 184 | #include <boost/config.hpp>
#if defined(BOOST_MSVC)
#pragma warning(disable: 4786) // identifier truncated in debug info
#pragma warning(disable: 4710) // function not inlined
#pragma warning(disable: 4711) // function selected for automatic inline expansion
#pragma warning(disable: 4514) // unreferenced inline re... |
8ecfcd35ec94753fc5b7215f6e48f587087283e786f61e93f199403d937f6d79 | C++ | 5,525 | 237 | //
// sender.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 !def... |
2a7529c82a4b6cde52060f4b6a242b58adfc5bd68a8df98a73241247ec798858 | C++ | 5,528 | 152 | //
// callback_wrapper.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)
//
#include <boost/asio.hpp>
#... |
79691ff0de3a0193b9bce7c13784891cc8ff3fa804e3624ef74e9192186a7f6b | C++ | 5,531 | 160 | /***************************************************************************************************************
Copyright (c) 2011, Marco Reisert, Valerij G. Kiselev, Medical Physics, University Medical Center Freiburg
All rights reserved.
Redistribution and use in source and binary forms, with or without... |
594f95d2521de6acfdbfb734b0aa496031b803767d7706426cefb951031c4c05 | C++ | 5,536 | 229 | /*
*
* Copyright (c) 1998-2004
* 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 versio... |
89b2011575be40d5892d7d9165ae6cf633b3401a134d3fcacd74f4a32bff0749 | C++ | 5,537 | 212 | //
// third_party_lib.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)
//
#include <boost/asio.hpp>
#in... |
962e006d0e76986edc51e57ff40fd7d6c0969d7762dc52b7e7a98042c9f22a8b | C++ | 5,555 | 180 | //
// 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
//
//------------------... |
a4ceee8746e52697ce3389258251551ea5a560c3451fdfb6071280514c8ccf96 | C++ | 5,559 | 196 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// extended_type_info.cpp: implementation for portable version of type_info
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See a... |
06e0d12c2d5b0bfcb00b15746776940b97e9be4bca1b3a53b544e3e149f89031 | C++ | 5,570 | 188 | #include <boost/config.hpp>
#if defined(BOOST_MSVC)
#pragma warning(disable: 4786) // identifier truncated in debug info
#pragma warning(disable: 4710) // function not inlined
#pragma warning(disable: 4711) // function selected for automatic inline expansion
#pragma warning(disable: 4514) // unreferenced inline re... |
3052d253330cf4c83b284b69b3b968d8b2a9873b68ea1ce208d9e69464613ae4 | C++ | 5,582 | 154 | /*
* 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)
*
* Copyright (c) 2020 Andrey Semashev
*/
/*!
* \file find_address_sse41.cpp
*
* This file contains SSE4.1 implementation of the \c find_address algorith... |
3371f1ca27abe5efd8cff83a79baab0f5d69b59edb6c4a9bfeb8a081f899b170 | C++ | 5,593 | 242 | //
// server.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)
//
#include <cstdlib>
#include <iostream>
#include... |
91e3b5c012a3c48a2f5af2aae39603cd84c97f2116d0cb2efe14ed16278fb0e4 | C++ | 5,604 | 195 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// extended_type_info.cpp: implementation for portable version of type_info
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See a... |
97e1fbb06b4656b6142b50d89cbab7f6b49a4c0df6698c8526888682cd0a19b6 | C++ | 5,604 | 141 | // 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>
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify... |
71b7e5a1b5e48369953c17e5663fab524bb71e0e21b29b43253cf367a6eb9e13 | C++ | 5,617 | 154 | //
// bind_noexcept_mf2_test.cpp - noexcept member functions w/ the type<> syntax
//
// Copyright 2017 Peter Dimov
//
// 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/bind.hpp>
#include <bo... |
a0dd89e3cc86b7bfa0c69e62e27f1cb8862e05fe2e444149f38dcca4ba805e1a | C++ | 5,630 | 141 | // 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>
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify... |
9511f2c6caa6fe78c9d410f1185dc4e49512460751183ae4f5bbca0cbabdf909 | C++ | 5,637 | 196 | #include <boost/config.hpp>
#ifndef BOOST_MSVC
int main()
{
}
#else
#if defined(BOOST_MSVC)
#pragma warning(disable: 4786) // identifier truncated in debug info
#pragma warning(disable: 4710) // function not inlined
#pragma warning(disable: 4711) // function selected for automatic inline expansion
#pragma warnin... |
b8832403cae5d496fe04c91685b3df5cc2fa1e2dcd299a7e403b452eeea55e24 | C++ | 5,640 | 225 | //fast_marching.cpp
// this file is a C++ implementation of the fast marching method. The
// code in this file is independent of Python.
#include "base_marcher.h"
#include "heap.h"
#include "math.h"
#include <vector>
extern "C" {
baseMarcher::baseMarcher(
double *phi, double *dx, long long *flag,
double... |
f4542a7ec3b0a2026f21da3df6656de527ca51a0a68530c0a65c6a033a4ad8a1 | C++ | 5,640 | 154 | //
// callback_wrapper.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)
//
#include <boost/asio.hpp>
#... |
f1874feae537193bd5c673068fef79c90c771d64e1ee4b397117af298e0966bb | C++ | 5,691 | 130 | // 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 Daniel Gomez Ferro <dgomezferro@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public... |
46ddede74e503aaed0c5cbd5b3f053b8423f5a064bee5464b76ff655b5db10f5 | C++ | 5,695 | 123 | #include "SoloFeature.h"
#include "streamFuns.h"
#include "Stats.h"
#include "GlobalVariables.h"
void SoloFeature::statsOutput()
{
ofstream &strOut=ofstrOpen(outputPrefix+"Summary.csv", ERROR_OUT, P);
//Sequencing
strOut << "Number of Reads," << g_statsAll.readN <<'\n';
strOut << "Reads With Valid Barc... |
2696f11a7d1747f6ac3743b1011ecfb73e79b2467e0b7adcb373f3a02bd42ea5 | C++ | 5,706 | 130 | // 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 Daniel Gomez Ferro <dgomezferro@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public... |
c3ec104a8d3fcad0e10bc647f81228eca9f3a472d1d985f09aa30306e1d5c977 | C++ | 5,706 | 176 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com>
// Copyright (C) 2010 Hauke Heibel <hauke.heibel@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesse... |
e233242bf69585fc1e4458643a266faa13ab12f94b02c9fc328bb8b3abe12265 | C++ | 5,707 | 165 | #include <stdint.h>
#include "../../include/lsl_cpp.h"
#include <boost/chrono.hpp>
#include <boost/thread.hpp>
#include <boost/bind.hpp>
#include <boost/lexical_cast.hpp>
#include <iostream>
#include <map>
#include <time.h>
#include <stdlib.h>
using namespace std;
// set to true by the main program when we're ready to... |
0b3910540063e8081357f45b66881428593f40bb53226de86131f745b8b8b13b | C++ | 5,715 | 196 | #include <boost/config.hpp>
#ifndef BOOST_MSVC
int main()
{
}
#else
#if defined(BOOST_MSVC)
#pragma warning(disable: 4786) // identifier truncated in debug info
#pragma warning(disable: 4710) // function not inlined
#pragma warning(disable: 4711) // function selected for automatic inline expansion
#pragma warnin... |
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