sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
66f8d8b1f4f15f61450b9a7f9f9d8affd517e22d0dcb4525d6ae8956216989dc | C++ | 4,519 | 181 | #include <boost/asio/execution.hpp>
#include <condition_variable>
#include <iostream>
#include <memory>
#include <mutex>
#include <queue>
namespace execution = boost::asio::execution;
namespace custom_props {
struct priority
{
template <typename T>
static constexpr bool is_applicable_property_v =
e... |
0365ef78e37564466a149646a909fcaf4d24a0bf45a600c33983ed7395cb8564 | C++ | 4,520 | 154 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// archive_exception.cpp:
// (C) Copyright 2009 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
// htt... |
33fa3dbaa24e61d0c35a59b61586c3aca15de91a9d0b2606afd1e4120ca124bf | C++ | 4,527 | 145 | // 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 ... |
76aa9321c3cf63cc45acd8c16d0b841faec1b9b0aac3e78bbdea865867da9538 | C++ | 4,534 | 124 | #include "ReadAlign.h"
#include "readLoad.h"
#include "readBarcodeLoad.h"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
#include "GlobalVariables.h"
int ReadAlign::oneRead() {//process one read: load, map, write
//load read name, sequence, quality from the streams into internal arrays
int readStatus[P.r... |
183d8ec51884f048c335518c125aed6cf5c2929fece74e7ad76d99b542ed369c | C++ | 4,542 | 165 | #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... |
b173bbeb34b570069a348874460e0b42c74f81c8f0f78ffb1f507f9b49a68dd1 | C++ | 4,549 | 105 | /*
Copyright (c) Marshall Clow 2010-2012.
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/none... |
0f99af5d6560bb6ccd2aac2f68a8ecc37c1f1b510e72bdd3bda48688479dbadf | C++ | 4,556 | 128 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010-2011 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 Sof... |
245ef84c964a01377aa5c2a1761e4627797f828fac1e65e67f859f35cf034552 | C++ | 4,560 | 91 | // 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... |
23a2dde329767bc2b07a5226aceb2a8f514ba82bc8a34aaa95fdeddeb4c76ce3 | C++ | 4,593 | 217 | //
// 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 <array>
#include <cstdlib>
#include <i... |
0c804cba4699533bc9f27e235c3ed762b0a95eab45877421bad38f3da4569c0b | C++ | 4,605 | 165 | #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... |
9dd0636c47f5f453730eca6ca4471b0a4a2e83033625cd5a211ed19495edac8d | C++ | 4,622 | 154 | //
// bind_noexcept_mf_test.cpp
//
// 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 <boost/ref.hpp>
#include <boost/core/lightweight_test... |
f3476afa2f0a380fd944903775ecd9f4c63df97fcf29d74e4d5141c5098009bd | C++ | 4,631 | 177 | //
// transmit_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)
//
#include <ctime>
#include <iostre... |
78c14106921b146d58fd0199950297acb8a70ecd1f122bacf7b68b5205be136e | C++ | 4,648 | 218 | /*
------------------------------------------------------------------
This file is part of the Open Ephys GUI
Copyright (C) 2017 Open Ephys
------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Pub... |
882ba10e157dfb177380183d1797bbd81078333b797aea30addbb6dc8522376b | C++ | 4,656 | 147 | #include <asio/io_context.hpp>
#include <asio/ip/address.hpp>
#include <asio/ip/tcp.hpp>
#include <asio/read.hpp>
#include <asio/signal_set.hpp>
#include <asio/steady_timer.hpp>
#include <asio/write.hpp>
#include <chrono>
#include <cstdint>
#include <iostream>
#include <list>
#include <signal.h>
#include <string>
// L... |
2e985461411b6f2613198cd3343ecc93545fba583e1b382feaa2c95f67f2ca86 | C++ | 4,658 | 122 | //
// 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 "server.hpp"
#include "request.hpp"
#i... |
696023e6827042ec507cf2ac4d84443643a50e598fbcc37831e00ae133bc5fc2 | C++ | 4,658 | 100 | #include "readLoad.h"
#include "ErrorWarning.h"
int readLoad(istream& readInStream, Parameters& P, uint& Lread, uint& LreadOriginal, \
char* readName, char* Seq, char* SeqNum, char* Qual, vector<ClipMate> &clipOneMate, \
uint &iReadAll, uint32 &readFilesIndex, char &readFilter, string &readName... |
873b73210b4cc172f26cf45a10a74f6f1c5961c237fdb88c805ff136ddde5cef | C++ | 4,671 | 168 | // Boost.Assign library
//
// Copyright Thorsten Ottosen 2003-2004. 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)
//
// For more information, see http://www.boost.org/libs/ass... |
f11d811e413c0328141e41a783f41bf39ba15d72f534db36eafbb4c2969907db | C++ | 4,671 | 175 | #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... |
0f13e6329cad7f76d3d09b257b59e5018693ab9911911107c97214da84baee9d | C++ | 4,674 | 124 | // (C) Copyright Eric Niebler, Olivier Gygi 2006.
// 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 p_square_cumul_dist.hpp
#include <cmath>
#include <boost/ra... |
697cd9675530ac4ca0a8320be8f16c0bfbbc2e3d8d7d91152b7acc5db5170475 | C++ | 4,691 | 135 | // 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... |
28d049c76b695a45a4b196c1865592e661ae5c8147924c1954f6f1b1e28a1f7f | C++ | 4,695 | 159 | //
// stream_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 autolinking for unit t... |
8c941dcd893edd7774760095d02621e831a85e51edfa64cd3e6b77ac5eeaca15 | C++ | 4,699 | 105 | // Copyright 2013 Krzysztof Czainski
// Copyright 2013 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)
/*
* @file chrono_rounding.cpp
*
* @since 2013-11-22
* @author Krz... |
c222d7f923c57652abf3fa4cf734a86ffacd5453ccdb4fbfbcca9852d40c5b15 | C++ | 4,711 | 125 | #include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"
ReadAlign::ReadAlign (Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, int iChunk)
: mapGen(genomeIn), genOut(*genomeIn.genomeOut.g), P(Pin), chunkTr(TrIn)
{
readNmates=P.readNmates; //not r... |
eee19057db907e4b0b709a190b64183330b0ced27df46ab7b6226534df693459 | C++ | 4,711 | 172 | //
// 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 ... |
19366f47d49f9d9b1759ecbb75c2c929a7f8c22a2a85b0eaacb744180dd087ad | C++ | 4,714 | 123 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2006-2008 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 Publ... |
7db213fd0e378376f39967bfd4df43b8cff5fbe15ced8aa514b2ca279380f447 | C++ | 4,720 | 153 | //
// 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
//
//------------------... |
c46e8fd06797c9947a45b05c3ae18a9a59c18335e4918b5c4e42f26b7eb9f390 | C++ | 4,722 | 135 | // 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... |
0d6cb4559165ac58ff9248b7d88e1d1850209132d7c50871d8e44409b0adb961 | C++ | 4,728 | 161 | #include "threadconfig.h"
#include "util.h"
ThreadConfig::ThreadConfig(Options* opt, int threadId, bool paired){
mOptions = opt;
mThreadId = threadId;
mWorkingSplit = threadId;
mCurrentSplitReads = 0;
mPreStats1 = new Stats(mOptions, false);
mPostStats1 = new Stats(mOptions, false);
if(pair... |
fdc73f7838d5813e586a1e666e122a802064ffae5fe5435033a1cd17a1898520 | C++ | 4,734 | 153 | //
// 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 ... |
e8ae1f3694fe505141e0c1d81e7f8766822714614139bb413e608709cb07b618 | C++ | 4,735 | 123 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2006-2008 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 Publ... |
5c08f709891cd7d60238b6569fc48815f22357a66efa748b3e2fea1cd9a47622 | C++ | 4,738 | 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... |
6d86dc35972db47e5d38a8c35220a3cb6cf3d707f3318e59d2f5de8657f80940 | C++ | 4,740 | 197 |
#include <include/matlab_bgl.h>
#include <stdio.h>
#include "libmbgl_funcs_test.h"
int test_1() {
// line graph
const mbglIndex n = 10;
mbglIndex rp[] = {0,1,3,5,7,9,11,13,15,17,18};
mbglIndex ci[] = {1,0,2,1,3,2,4,3,5,4,6,5,7,6,8,7,9,8};
mbglIndex i[3*n-6];
mbglIndex j[3*n-6];
mbglIndex extra_edges;
... |
b67f38ff48acc3f1c4ae7208ee7c8e544dd8011ce6518051a3e6231ffb738645 | C++ | 4,743 | 163 | //
// ping.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>
#include <boost/bind/bind... |
1800d4b0f8432ab22856c6fd5a0c15cd2f9c0d165867fa2ae60e91b488c788bb | C++ | 4,746 | 134 |
#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 benchVec(MatrixXf& a, ... |
3b6b19e69e25f14e00dc72613eddd5b36d223b1672900a84acf6f3ca56c88fbf | C++ | 4,749 | 206 | //
// 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 ... |
ae124ffba531e2bcc56d5a9386916aed5a4b43ab29ec9a813936449bcc8dbacf | C++ | 4,751 | 112 | #include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "SequenceFuns.h"
#include "systemFunctions.h"
void SoloFeature::countCBgeneUMI()
{
time_t rawTime;
rguStride=2;
if (pSolo.readIndexYes[featureType])
rguStride=3; //to keep readI column
if (pSolo.readI... |
8d2d5a93b7f6b6dfad8b92c14572db66544e39d9f4512bc40595ae0de2d7ea77 | C++ | 4,753 | 131 | // (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 pot_quantile.hpp
#define BOOST_NUMERIC_FUNCTIONAL_STD_COMPLEX_SUPPORT
#de... |
cdd8d880e81434a5030f3fe7937431ac00f9f9f51714fdd2a647291a673c24df | C++ | 4,767 | 145 | //---------------------------------------------------------------------------//
// Copyright (c) 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://boostorg.gi... |
56cc74dd44ad22b8f255e193eef6548771e382b715b48efcfe8228e13af1a232 | C++ | 4,768 | 166 | /**
* Copyright 2017-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the license found in the
* LICENSE file in the root directory of this source tree.
*/
#include <torch/extension.h> // @manual=//caffe2:torch_extension
#include <algorithm>
namespace {
template <typename T... |
39dec8728d36cbac599d0e3f0e7edee4637b5849884bbb6e8402703e2d0c2855 | C++ | 4,769 | 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>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
1b45a72aefac33d042dbefc2b861c646be817eb3fbf59738d6f746594dd03d65 | C++ | 4,775 | 202 | //
// prioritised_handlers.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/asi... |
0a1bd1564f42d75c132df0676f2e6c208003e50ae945b3e02d62f5fbc5ad32f1 | C++ | 4,780 | 148 | /***************************************************************************************************************
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... |
84bb728fa727d48ee51f72fef915f5fbc618e079842a155d66bb504e91dacc17 | C++ | 4,782 | 136 | // 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... |
885654629c77b82abdbd0b71824ee7573d72fb871c3df27ee4740bd1cc67f267 | C++ | 4,785 | 120 | // 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 ... |
928feb10a3f5c4d95557567bcdb19ce4e7765392b1169efab682a806632eedab | C++ | 4,787 | 118 | // 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... |
3e126d04c214f45912eef5250bdc304f325bd49ffdcf27f5e3a6770797775b45 | C++ | 4,794 | 107 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
8304c58bcf6003b411379d8c985178b95c43dc1c42e120109dec432b389d704f | C++ | 4,794 | 98 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
32a2cb40c1e00e3197d4619c1c5f35a775df2e0ea646197f41e9b66da4e501f2 | C++ | 4,799 | 147 | /**
* @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... |
9a4a95c7d8cf52d1e0df61e34f2ae268190c3fdbab41cf6ed6062b7ab0178ffb | C++ | 4,801 | 93 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
aa1de56f17db784f90ce3c1b32beb605eaa343e43d3d0bb971309756c960367d | C++ | 4,806 | 156 | //
// 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 ... |
f751382276b24ba544c24f86d8adaf99688c4769f8ffbf437dad25ed2466a540 | C++ | 4,811 | 208 | //
// bind_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 t... |
d9aa60ea1ae0034911a09f177f89e20d7aac32282e3ee72aed67f28107bcc359 | C++ | 4,818 | 97 | #include "bamSortByCoordinate.h"
#include "BAMfunctions.h"
#include "BAMbinSortByCoordinate.h"
#include "BAMbinSortUnmapped.h"
#include "ErrorWarning.h"
#include "bam_cat.h"
void bamSortByCoordinate (Parameters &P, ReadAlignChunk **RAchunk, Genome &genome, Solo &solo) {
if (P.outBAMcoord) {//sort BAM if needed
... |
99f490aa5e66510ee6d72a355704de091e92f8b4bf8cbb580f4b914189db1a79 | C++ | 4,819 | 116 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2006-2008 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 Publ... |
09eb882afb1d5f797c7c226ffc6a97eee7f59e91cecbebc2a6887159984c9dc7 | C++ | 4,830 | 195 | //
// 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 ... |
990fa1b2494a9e994682058adc7ba58b168092baaf9c72502193fdcfa1eec9b0 | C++ | 4,854 | 137 | // 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
//... |
c4e370d1093f6f4b1237eaed916aad28862756b99881e5019b3da2db593f71cb | C++ | 4,860 | 167 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// extended_type_info_typeid.cpp: specific implementation of type info
// that is based on typeid
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// Licens... |
118f2da879af9d28778c7749f9e678f33fc1d415e15b6a49ae20dafe26bbc73b | C++ | 4,861 | 143 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
// Copyright (C) 2009 Ricard Marxer <email@ricardmarxer.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU... |
62dcfb801dbd84144579706b09f440fb4b5a1f393fa8301866f4ab38dac6079c | C++ | 4,864 | 192 | //
// 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 ... |
cdf9d093d6ee02fb2453f19214c010fb3aaae9f10ff78eaf8512b5903d30a5ad | C++ | 4,874 | 276 |
#include "mex.h"
#include "matrix.h"
#include <math.h>
#include <map>
#include <vector>
#include <string.h>
using namespace std;
#define REAL float
#define PI 3.1415926536
#include "MersenneTwister.h"
MTRand mtrand;
#include "ParticleGrid.cpp"
class ParticleL : public Particle
{
public:
int label;
int nume... |
02982843eef0ecba88cc8b1315f32ad9740e7b152da0b1287209204bd5273540 | C++ | 4,877 | 114 | /*
Copyright (c) Marshall Clow 2010-2012.
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/any_... |
9a31f9ef8c927e77b674ed7b4bc9e0a1db4d961141bdd9611e70402e932b9f77 | C++ | 4,877 | 147 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2006-2008 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 Publ... |
cdff4d368b127cab3e9e3cdb3c09708940472d12f3c43fa271dbeb048f3ba6b6 | C++ | 4,889 | 115 | #include "ReadAlign.h"
#include "SuffixArrayFuns.h"
#include "ErrorWarning.h"
uint ReadAlign::maxMappableLength2strands(uint pieceStartIn, uint pieceLengthIn, uint iDir, uint iSA1, uint iSA2, uint& maxLbest, uint iFrag) {
//returns number of mappings, maxMappedLength=mapped length
uint Nrep=0, indStartEnd[2], ... |
dbdd2be3aaab48b04b118be1303bcdf9db17084bf250ee5fcb7e5c7c1a92cc90 | C++ | 4,892 | 147 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2006-2008 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 Publ... |
685a15baba6ea265ec53b3bcbec904b8e755e2cbc9403d61697474cdb17aee97 | C++ | 4,894 | 167 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// extended_type_info_typeid.cpp: specific implementation of type info
// that is based on typeid
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// Licens... |
5e8d65e2b9bb761b381b963bc18859c9d4995ee5c0529d8f17f4412956442e9c | C++ | 4,900 | 155 | //
// composed_1.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/deferred.hpp>
#inc... |
0349b1056f5af892a1e088ca3f242c94f1858ec1c7707bca9995212b6a97cd3b | C++ | 4,912 | 178 | //
// experimental/coro/cancel.cpp
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
//
// Copyright (c) 2021-2022 Klemens D. Morgenstern
// (klemens dot morgenstern at gmx dot net)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boo... |
1d2b667539f952c10a020c9ef814b046938d52f8805acd278f38c30e23c2e3a6 | C++ | 4,920 | 171 | //
// unicast.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 !d... |
7963efae402892a3c98e000e6ebc679797fe51c57bf832a8461a4939257a5530 | C++ | 4,922 | 200 | // 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... |
c2636423989d2c161ad9a4a22abd311449319f5a1f3292ba7a0d01a4eed3d59d | C++ | 4,924 | 116 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2006-2008 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 Publ... |
73c965fcd326cd7e66eed334732bdae0a13737bdc18d86bfed213ab9a9fca3f7 | C++ | 4,926 | 123 | /*
Copyright (c) Marshall Clow 2010-2012.
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
Testing the range-based interfaces
*/
#include <boost/algorith... |
caa4e53c25db3c7de9f279cb36c5e376b87db72cc5d15cc18a7e1f30f19dae96 | C++ | 4,926 | 147 | // 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... |
079ac027ed90c458a3380a95f368bd41c637d0188f04cb058c397bec8bd3de47 | C++ | 4,942 | 162 | #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... |
8d5bd6f1f4f0f5f8d394cb8369dc452c7c3905261a68f94e707f0b415a814ec0 | C++ | 4,947 | 174 | //
// 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 ... |
5bf88f62bfc677cd8c77de59945a661b4e523a1b7cac03dd463e9db8c35a2368 | C++ | 4,954 | 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 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
//... |
7d293aa1a12c060649569f3741ffa0642ec7e36979dd0a58d4f09f393066a8e6 | C++ | 4,956 | 147 | // 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... |
83b93b0bdde110da9d1f8704e6002a7a6537c966a52d71e6cc273dfb8b966b12 | C++ | 4,966 | 176 |
/** @file spanning_trees.cc
* @author David F. Gleich
* @date 2008-09-29
* @copyright Stanford University, 2006-2008
* Implement the BGL spanning tree wrappers.
*/
/** History
* 2006-04-20: Initial version
* 2006-11-10: Fixed bug with incorrect number of edges returned,
* when the input graph has multipl... |
f565880cb58de14ee910ba540bd1b5513c9c1e7677114991d3e721878de20ec0 | C++ | 4,967 | 227 | //
// chat_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 <deque>
#... |
1e0383cf8ec87833993796388329b7697af2043eca5324034c60b3efd2f8c6ff | C++ | 4,969 | 123 | #include "OutSJ.h"
#include "ErrorWarning.h"
OutSJ::OutSJ (uint nSJmax, Parameters &Pin, Genome &genomeIn) : oneSJ(genomeIn), P(Pin), genOut(genomeIn) {//do I need P?
//data = new char [oneSJ.dataSize*nSJmax]; //allocate big array of SJ loci and properties
Nstore = nSJmax;
dataVec.resize(oneSJ.dataSize*N... |
f0c82af91c446d650de1ea2ea637374151a151c8bffc453cc4a6cae771063a91 | C++ | 4,971 | 142 | // 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 ... |
c444f0eec8b06b0244763d98ba15e27ee254abf1920f7931e68ce54ef1591f03 | C++ | 4,974 | 167 | //
// 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 ... |
2afc18c7a83e35e5916fd97f3273bf0cabe31196becac4fc411ea431e970a539 | C++ | 4,983 | 222 | //
// chat_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 <deque>
#... |
ea6a4186f2d1275b64a879b54dafc694924a0c3c2614178e33b8ea099fe97dcf | C++ | 4,992 | 140 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
f7989ccf7a965fd7c5801096e41c8cee2ed8ee93e5da5c67bcf969ccf009f395 | C++ | 4,995 | 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
//
//------------------... |
66e128ea6235d592ae6652daf0f75666525cc85b4eb1e3f9029a25e857710040 | C++ | 5,008 | 157 | //
// composed_1.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/deferred.hpp>
#inc... |
d48d64e7ba78d6d13382e0fdb93ab9641486251e77d56e3bf2cf5c67e8fc98ba | C++ | 5,014 | 126 | #include "Chain.h"
#include "streamFuns.h"
#include "serviceFuns.cpp"
Chain::Chain(Parameters &Pin, string chainFileNameIn) : P(Pin), chainFileName(chainFileNameIn)
{
chainLoad();
};
void Chain::chainLoad()
{
ifstream &streamIn = ifstrOpen(chainFileName, ERROR_OUT, "SOLUTION: check path and permission for the... |
0fed80687f9ee71db8385de4d496ac82bccf59ff05efbc1cdeb5c3288e50fa39 | C++ | 5,015 | 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) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2010 Jitse Niesen <jitse@maths.leeds.ac.uk>
//
// Eigen is free software; you can redistribute it an... |
ffa8f15fc48a8072032c710456835a0587f8d746be51717f4f0991df8ca43ace | C++ | 5,020 | 170 | #include <boost/config.hpp>
#include <boost/algorithm/sort_subrange.hpp>
#include <boost/algorithm/cxx11/is_sorted.hpp>
#define BOOST_TEST_MAIN
#include <boost/test/unit_test.hpp>
#include <vector>
#include <iostream>
#if (__cplusplus >= 201103L) || defined(BOOST_NO_CXX98_RANDOM_SHUFFLE)
#include <random>
std::defa... |
6d95be32acd4fd0529ebb6243111369d26bdd7fd24976e5c4ea313a1708adcca | C++ | 5,028 | 153 | #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... |
0f0bfe2ead8180e5094114900c4506c82bd7a4c0a5d6943205a8f66d89f8ae2d | C++ | 5,047 | 147 | // 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) 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 ... |
2cfd32239d92244f07a854593ab465b6014645b217ef6c1b811ffb80c476bc18 | C++ | 5,048 | 104 | // This file is triangularView 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 b... |
46e5bb9dbe48396f3b869e537b4f88ff4b0722324a652f936537ec9b27f26821 | C++ | 5,055 | 104 | /*
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_cv.hpp>
#include "test.hpp"
struct... |
420b0c6efae15662dabe1e9b43fcdcd23980797f7cb54a68e3617b8410680f7a | C++ | 5,058 | 159 | //
// composed_1.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/deferred.hpp>
#inc... |
ccebb6393a5a8468399f7e511219b667a2233f82312ce59834a4bb0997d8700e | C++ | 5,065 | 145 | // Copyright 2009 Google Inc. All Rights Reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and ... |
64a0f8e3e58e65dfaf774cf28e2a53437b9fca1dbc6df617a735a5b31c2fd312 | C++ | 5,069 | 137 | /*
Copyright (c) Marshall Clow 2017.
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 <vector>
#include <functional>
#include <numeric>
#include <... |
ed7791fdba252de6bfa1e7afe9502ba2afc92ceea23eec1b37eb9ffb31a1fcad | C++ | 5,069 | 192 | #include <stdio.h>
#include <stdlib.h>
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <string.h>
void lowPass6yDecY(float* sptr, float* rptr, int w, int hs);
void lowPass6xDecX(float* sptr, float* rptr, int ws, int h);
void double2float(double *a, float* b, int N) {
int i; for (i=0;i<N;i++) b[i] = (... |
2d1f4c727c8e51eb2763a0559cc47683fc5923acc160d85092a6033724d08f89 | C++ | 5,070 | 130 | // 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) 2010 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 L... |
cda3d168607058d8b2de86e8e10c99d58b01aac824f5014296ef884b93935319 | C++ | 5,075 | 138 | //---------------------------------------------------------------------------//
// 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... |
c6077a5363cf6f8276c3353b93e1bca44276f72c8e1a81deffb83a796a7b338e | C++ | 5,084 | 166 | // 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... |
39e5dfbcd32b45653639d18eef8051383b38ad1d7eee4df7d3e015cc4fc5ad29 | C++ | 5,089 | 153 | //---------------------------------------------------------------------------//
// 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... |
e81dc1517164878e63936eb4318d6536139e16b547be0f8c1db1583b3eb0edf2 | C++ | 5,090 | 192 | // Copyright 2003-2008 Jan Gaspar.
// Copyright 2013 Paul A. Bristow. Added some Quickbook snippet markers.
// Distributed under the Boost Software License, Version 1.0.
// (See the accompanying file LICENSE_1_0.txt
// or a copy at <http://www.boost.org/LICENSE_1_0.txt>.)
//[circular_buffer_bound_example_1
/*`
This e... |
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