sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
078ec05edb1e85c01f31f372e79a766f13355f59294b36a99273d0ba7736c9cd | C++ | 6,472 | 203 | //
// stream.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... |
0566b7915622231c37ed2174e2b4dff6e901eda55535f452303ade5b98ad016a | C++ | 6,489 | 124 | // Distributed under the Boost Software License, Version 1.0.
// Copyright 2011 Vicente J. Botet Escriba
// See http://www.boost.org/LICENSE_1_0.txt
#include <boost/chrono/chrono_io.hpp>
//#include <boost/chrono/io/duration_units.hpp>
#include <sstream>
#include <boost/detail/lightweight_test.hpp>
template<typena... |
8d769ca7f9cb2ce64b98717ab1c0dd1c4408f8ca28935b0fec98e5f66aa0ced6 | C++ | 6,501 | 162 | /*
Copyright (c) Alexander Zaitsev <zamazan4ik@gmail.com>, 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)
See http://www.boost.org/ for latest version.
*/
#include <vector>
#include <boost/algorithm/ap... |
c4dbd9342ab970d9bc345f130fcfc11c839335931c40153b410ec6a2c46d9019 | C++ | 6,516 | 167 | #include "Transcript.h"
#include "binarySearch2.h"
bool Transcript::transformGenome(Genome &genOut, Transcript & A)
{
uint32 nB=0;//number of out blocks
auto &coBl=genOut.genomeOut.convBlocks;
//uint64 icb=0;
//auto cBit=coBl.begin();
for (uint32 iA=0; iA<nExons; iA++) {//loop over blocks... |
65a40cedd3271d845a4a2ad76fba9e0cd6683c1ef763b08d37700660927cdca1 | C++ | 6,535 | 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 <gael.guennebaud@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Publi... |
e4e1e31b56556f453f0296476255cb2eec288e61a12707061275996619ec8b85 | C++ | 6,542 | 156 | // 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>
//
// 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... |
7e004ab84473afa1d914fce54c4ee7b1a92e7ae6d5058f840d7c19af29978cd4 | C++ | 6,550 | 181 | #include "ChimericAlign.h"
void ChimericAlign::chimericStitching(char *genSeq, char **Read1) {
if (stitchingDone)
return;
stitchingDone=true;
char *readSeq=Read1[0]; //only direct read sequence is used - reverse complemented if necessary in the algorithm
al1=new Transcript(*al1);
al2=ne... |
7d6b8579fe2d5fc24c7c7c2928ab35258a93379929d695d437bd363c4e61af05 | C++ | 6,563 | 222 | //
// 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 ... |
c22ce900ef92e9d3d293e0f1072a44f31f24c65208283dddf40da2c65f480198 | C++ | 6,579 | 191 | // Copyright 2007, 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 ... |
8e06954287d0a38e31aba63a90d036708ae6d0125f32cbfb5da6a947d123062e | C++ | 6,588 | 153 | /*
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/algorithm/searching/boyer_moore.hpp>
#include <b... |
73646d9038873a68bb2e56b12495d7f7b65b5c23901109701da446af454ba2ec | C++ | 6,593 | 199 | // 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 ... |
277d71c59f829f7f33a8df4159a02cfaae81f76914e51e1be406ca55cf7e4821 | C++ | 6,594 | 156 | #include <cmath>
#include <iostream>
#include <map>
#include <cstring>
#include <lsl_cpp.h>
#include <thread>
#include <algorithm>
#include <random>
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
// define a packed sample struct (here: a 16 bit stereo sample).
#pragma pack(1)
struct stereo_sample {
int16_t ... |
a846a2a2a2a944512af5d12e94413f8c8795c2db347083c3962dee832d9b1222 | C++ | 6,595 | 182 | // test_system_clock.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... |
1bf9b5599045606910271772bb6010ffe4b8b85b96c3ce90f1c1fd3cb17734a5 | C++ | 6,623 | 153 | /*
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/algorithm/searching/boyer_moore.hpp>
#include <b... |
8eda600cc1c9541a356da3a48a633ee3647b4f135dcf24dde246d10f0323bd5c | C++ | 6,623 | 237 | // timeval_demo.cpp ----------------------------------------------------------//
// Copyright 2008 Howard Hinnant
// Copyright 2008 Beman Dawes
// Copyright 2009 Vicente J. Botet Escriba
// Copyright (c) Microsoft Corporation 2014
// Distributed under the Boost Software License, Version 1.0.
// See http://www... |
2b85eddf25b0a94d6fc62d3ec04231302364ae9b45d36072c09e0ccfa3ab5e51 | C++ | 6,635 | 266 | //
// experimental/coro/simple_test.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... |
e75448e32d95e3d89526d839fbdadecf38549df398264088c4797e5bff7f20c2 | C++ | 6,651 | 173 | //---------------------------------------------------------------------------//
// 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... |
100f8b541b8d484d54954e630048df3d0cb9a0c596e461b3960b938e805f3469 | C++ | 6,678 | 241 | //
// 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... |
49dac62fe9d7dab3610bb70b4387d1cf1a3298b32aafa8c727a9940a5fabc7b8 | C++ | 6,678 | 198 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2009 Hauke Heibel <hauke.heibel@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// L... |
c75c8506f1a736a8cbbe71cf8cae6bd03f3f6d172ffb03a9e3db46585cbbe807 | C++ | 6,678 | 165 | //---------------------------------------------------------------------------//
// 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... |
eb8ed5afc6e6ccd2f1b50738f494f758648fe6f18e1cc33006121969337719f5 | C++ | 6,678 | 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) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// m... |
a7b283aeed40ff27018f5ce37fadfdd24c9efb49369ff3ac871a0f3cfad116e7 | C++ | 6,696 | 243 | //
// 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/conf... |
f050f06e1733540576fe33c8dbc1ee7467f38f4ba419564403eceda5bb564300 | C++ | 6,697 | 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) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// m... |
5ceb1cdf3ba80dad7b1afca694bab8c8dc1d2dc71376596e2362ba8743fb661e | C++ | 6,705 | 159 | // 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... |
612ef792751b6b5db7b2b311db68b8ea52318fbad1773f5eebaeea75a66f5014 | C++ | 6,705 | 159 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
b7f26034827ebb390ca42d41fc776cb873f56267d521d1581f1f427f6652bcd5 | C++ | 6,722 | 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) 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 ... |
5e9276421b74f2e94dd05df734254518fcaa754228a54eacd62a753fa472335f | C++ | 6,724 | 172 | // 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 ... |
d48bba6f2652f5acc7180f4d926a2bfe7c414cb9b61fe0eaa42e35ce6ea952ae | C++ | 6,730 | 187 | #include "udp_server.h"
#include "socket_utils.h"
#include "stream_info_impl.h"
#include <boost/asio/ip/address.hpp>
#include <boost/asio/ip/multicast.hpp>
#include <boost/asio/ip/udp.hpp>
#include <loguru.hpp>
#include <sstream>
namespace lsl {
namespace ip = asio::ip;
using err_t = const lslboost::system::error_code... |
e2f82765ab24d46abffa93c51e796e0e9fb3d94bbfe071ff9344b0173d9bb298 | C++ | 6,734 | 127 | #include<string>
#include<stdlib.h>
using namespace std;
# define gr (double)1.0
double vl_sec(double v, double gam);
double ac_sec(double a, double a_de, double a_de_s, double Dif, double rv, double gam, double Pf_s, double Pr_s);
int main(int argc, const char* argv[])
{
/*
para:
para[0]=gf, para[1]=... |
a8aae305ca147e36dfe75396e32885bb01792aafd80534dbd8f19b410efd6368 | C++ | 6,737 | 303 | #include "node.h"
#include "token.h"
#include "scanner.h"
#include "content.h"
#include "parser.h"
#include "scalar.h"
#include "sequence.h"
#include "map.h"
#include "aliascontent.h"
#include "iterpriv.h"
#include "emitter.h"
#include "tag.h"
#include <stdexcept>
namespace YAML
{
// the ordering!
bool ltnode::opera... |
47c0f79dcbdc3420b5cccb1762a14e2893334ce519e608dff02f88f263cf3d36 | C++ | 6,743 | 248 | // 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... |
ca7faa893c749db90777b2e5c48ddb56bb91c5159483ba22c0cd36b5e295df92 | C++ | 6,743 | 194 | #include "BAMfunctions.h"
#include "htslib/htslib/kstring.h"
string bam_cigarString (bam1_t *b) {//output CIGAR string
// kstring_t strK;
// kstring_t *str=&strK;
const bam1_core_t *c = &b->core;
string cigarString("");
if ( c->n_cigar > 0 ) {
uint32_t *cigar = bam_get_cigar(b);
for (in... |
544d8863c178f81f19629fc008114c43abde1d6cac907f3f40c758abd5ef3c62 | C++ | 6,745 | 279 | // 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... |
4400cb994a810fa2a6e24235aa7b74f5307c503276f037327dd0acf62d11004d | C++ | 6,770 | 279 | // 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... |
24a27c6466dcafac2fb45968e39a48f08c78866952752828f4e897f4005103d6 | C++ | 6,812 | 161 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 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 Softwar... |
bb34432bbf79a276ed0cc691439c0be258f07a3052c61473433c66f36939f608 | C++ | 6,824 | 161 | // 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... |
e27e8ec505f05f073e16e606a04e0817e6432c60e94d04d4d3c30e6a09613b84 | C++ | 6,824 | 128 | #include "ReadAlignChunk.h"
#include "GlobalVariables.h"
#include "ThreadControl.h"
#include "ErrorWarning.h"
#include SAMTOOLS_BGZF_H
void ReadAlignChunk::mapChunk() {//map one chunk. Input reads stream has to be setup in RA->readInStream[ii]
for (uint32 im=0; im<1; im++) {//hardcoded mate 1 5p onyl for now
... |
d5acbed4669e4521211063fc9d5917c51dfccbe537f53752a7aa15c502a62d45 | C++ | 6,860 | 206 | /*
*
* 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.
... |
8700c9e3f17f32fb7476389a73cf1cebd0bf8e26634938a721c9bfb25170262a | C++ | 6,878 | 214 | #include "writerthread.h"
#include "util.h"
#include <memory.h>
#include <unistd.h>
#include <fcntl.h>
#include <cerrno>
#include <cstring>
#include <thread>
#include <chrono>
WriterThread::WriterThread(Options* opt, string filename, bool isSTDOUT){
mOptions = opt;
mWriter1 = NULL;
mInputCompleted = false;... |
0b458a0d9c6abadd7cc6d27039e29aa5ab70aee4b19c6f9a2cc46a57c48623b3 | C++ | 6,887 | 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) 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... |
6fdcf73542c3ad98578ca5a1038174e986eb1ad3aed00f4fc9e2f02432e28638 | C++ | 6,895 | 198 | // simulated_thread_interface_demo.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... |
dd3b6779dcf72191df7593198d2b830678ae973b7d563d736e7823efe6b8803c | C++ | 6,908 | 238 |
// g++-4.2 -O3 -DNDEBUG -I.. benchBlasGemm.cpp /usr/lib/libcblas.so.3 - o benchBlasGemm
// possible options:
// -DEIGEN_DONT_VECTORIZE
// -msse2
// #define EIGEN_DEFAULT_TO_ROW_MAJOR
#define _FLOAT
#include <Eigen/Array>
#include <Eigen/Core>
#include "BenchTimer.h"
// include the BLAS headers
#include <cblas... |
2cf5525d721c96d083492db57def1d020ef1729072f9209b120ada88712a63bc | C++ | 6,912 | 201 | //===----------------------------------------------------------------------===//
//
// The LLVM Compiler Infrastructure
//
// This file is dual licensed under the MIT and the University of Illinois Open
// Source Licenses. See LICENSE.TXT for details.
//
//===----------------------------------------... |
6de88c9c5b7f6c14275c4c3aa06f424b3f93692d56eed7028175cff8359b0b53 | C++ | 6,916 | 236 | //---------------------------------------------------------------------------//
// Copyright (c) 2014 Fabian Köhler <fabian2804@googlemail.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://boo... |
1d69f8b3db6c0981317c2ad9feb8ea156c2d14c6e97435b3b6d4b997ade3ecaa | C++ | 6,923 | 192 | //
// client.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/lambd... |
a2233c991280e706906bb094432b364ca4d8a09db988417edb8651b47cfa110f | C++ | 6,929 | 237 | //---------------------------------------------------------------------------//
// Copyright (c) 2014 Roshan <thisisroshansmail@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... |
2b3603c7eff8c2f60713954553f41f0b68b2e62131eb3c35ca4f1b8441436338 | C++ | 6,931 | 284 | #include <boost/asio/associated_executor.hpp>
#include <boost/asio/bind_executor.hpp>
#include <boost/asio/execution.hpp>
#include <condition_variable>
#include <future>
#include <memory>
#include <mutex>
#include <queue>
#include <thread>
#include <vector>
#include <cctype>
using boost::asio::executor_binder;
using b... |
b26c589e33ab794f3ba91a6a3b7304a940a00a36bcb6b3ac35b8656caabbee45 | C++ | 6,938 | 180 | // 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) 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... |
7b7510fadf4955d2f934d23d652dbd35add832e50bdfcc98421fb9be4588d808 | C++ | 6,944 | 173 | // 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... |
fff615628749cb272297e5b083d23e675397f48c67aa1ff5e13d591884258b45 | C++ | 6,949 | 234 | // Copyright 2007, 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 ... |
02cb9a65ae1ef2adcdbc901f59823bba482bf9f4809ea28e700ce8df1e1b8f1f | C++ | 6,952 | 219 | #include <boost/config.hpp>
#include <boost/config/pragma_message.hpp>
#if defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
BOOST_PRAGMA_MESSAGE( "Skipping test because BOOST_NO_CXX11_RVALUE_REFERENCES is defined" )
int main() {}
#elif defined(BOOST_NO_CXX11_SMART_PTR)
BOOST_PRAGMA_MESSAGE( "Skipping test because BOOST_NO... |
7cb0a607bf6e2f29e5e4138ad27740e873eb7648bffdd85f903e1b4a36d38c37 | C++ | 6,960 | 219 | //
// stream_protocol.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... |
9e105862c5deb57abee9a037aa446e6ac19a2b2e0a26afa6619bbbbdb2ecf788 | C++ | 6,998 | 251 | //
// Copyright (c) 2017 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)
//
// Official repository: https://github.com/boostorg/beast
//
//--------------------... |
ae4cc400fc192a39ea1e8e362649fb77d34d7a9eff91261254be3624258ac4db | C++ | 7,008 | 190 | #include "Transcriptome.h"
#include "streamFuns.h"
#include "GlobalVariables.h"
#include "ErrorWarning.h"
#include "serviceFuns.cpp"
Transcriptome::Transcriptome (Parameters &Pin) : P(Pin){
if (!P.quant.yes)
return;
if (!P.pGe.transform.outQuant) {//standard
trInfoDir = P.pGe.sjdbGTFfile=="-"... |
02005bd7e8c86ed9607847a908d0f6a5b5c70c99145c348b09d9aec35aba22e7 | C++ | 7,009 | 172 | #include <cmath>
#include "SoloReadFeature.h"
#include "SoloCommon.h"
#include "SoloFeature.h"
#include "soloInputFeatureUMI.h"
#include "serviceFuns.cpp"
void SoloReadFeature::inputRecords(uint32 **cbP, uint32 cbPstride, vector<uint32> &cbReadCountTotal, vector<readInfoStruct> &readInfo, SoloReadFlagClass &readFlagCo... |
12b8e120b181964996f47177195bbe52a25cfdc605fa9614930a6a5cc9e00fcc | C++ | 7,010 | 186 | #include "BAMoutput.h"
#include <sys/stat.h>
#include "GlobalVariables.h"
#include <pthread.h>
#include "serviceFuns.cpp"
#include "ThreadControl.h"
#include "streamFuns.h"
BAMoutput::BAMoutput (int iChunk, string tmpDir, Parameters &Pin) : P(Pin){//allocate bam array
nBins=P.outBAMcoordNbins;
binSize=P.chunk... |
83d6c6e02ba913c0693fef34410ec551c8e41d54a1b5df7d569411b65a89c15f | C++ | 7,013 | 226 | //---------------------------------------------------------------------------//
// Copyright (c) 2013-2015 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... |
b35965f41bd65fb8124876a595fb0a50277014ad11d65f035ad115477d7b3aac | C++ | 7,027 | 172 | #include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "serviceFuns.cpp"
#include <unordered_map>
#include "SoloCommon.h"
#include <bitset>
#define def_MarkNoColor (uint32) -1
void collapseUMIwith1MMlowHalf(uint32 *umiArr, uint32 umiArrayStride, uint32 umiMaskLow, uint32 nU0, uint32 &nU... |
3d108260710811b22433dbf1e100b7333c4d057a1ddd002ed7ec9ff1106d41bb | C++ | 7,028 | 149 | #include "streamFuns.h"
#include "ErrorWarning.h"
#include <fstream>
#include <sys/statvfs.h>
#include <sys/stat.h>
#include <stdio.h>
#define fstream_Chunk_Max 2147483647
#include <cstring>
void createDirectory(const string dirPathIn, const mode_t dirPerm, const string dirParameter, Parameters &P)
{
string dirPath =... |
4d66081fbdb1851b0db15c132b9af7132c6cafa89a8587183175d1ad1094a7ac | C++ | 7,032 | 244 | //
// 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 ... |
0566a105fd1d3a430fcf0a6434fa3c31be8ed113fd79069a0cdf621a3cc026e0 | C++ | 7,050 | 288 | #include <boost/asio/associated_executor.hpp>
#include <boost/asio/bind_executor.hpp>
#include <boost/asio/execution_context.hpp>
#include <boost/asio/post.hpp>
#include <boost/asio/system_executor.hpp>
#include <boost/asio/use_future.hpp>
#include <condition_variable>
#include <future>
#include <memory>
#include <mute... |
9af017e0b9d5457822a4a80d76904272971c92ca61c114cabb6c0ddc87b0b986 | C++ | 7,054 | 171 | // This is the Mersenne Twister random number generator MT19937, which
// generates pseudorandom integers uniformly distributed in 0..(2^32 - 1)
// starting from any odd seed in 0..(2^32 - 1). This version is a recode
// by Shawn Cokus (Cokus@math.washington.edu) on March 8, 1998 of a version by
// Takuji Nishimura (w... |
d495532323c66c27e97158d2e38b4473e55e2f652f96418e6349d048ff5b2796 | C++ | 7,058 | 173 | #include "stream_outlet_impl.h"
#include "api_config.h"
#include "sample.h"
#include "send_buffer.h"
#include "tcp_server.h"
#include "udp_server.h"
#include <memory>
#include <sstream>
namespace asio = lslboost::asio;
namespace lsl {
stream_outlet_impl::stream_outlet_impl(
const stream_info_impl &info, int32_t chu... |
a47414199b35d1af47c49686effd11fa4c2becba1abc53c0b0be5984fad879e2 | C++ | 7,106 | 229 | /**
* @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... |
9850afef3bd3b0b40dbe91bca800b6eb6a6580004d712718945d122bc68e7f2c | C++ | 7,111 | 142 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <Rcpp.h>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(... |
0ca39eabd567f97eabceb767c7596fe1232223db7d8969f96c3fd2cd4f40816b | C++ | 7,118 | 177 | #include "stream_outlet_impl.h"
#include "api_config.h"
#include "sample.h"
#include "send_buffer.h"
#include "stream_info_impl.h"
#include "tcp_server.h"
#include "udp_server.h"
#include <algorithm>
#include <chrono>
#include <memory>
namespace lsl {
stream_outlet_impl::stream_outlet_impl(const stream_info_impl &inf... |
b17ae5f8099430a096e996d30bf499d4826fa773eb95279fa0d5b77d123eeed3 | C++ | 7,123 | 244 | //
// 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
//
//------------------... |
2175d6333ff64e4278d2fc1d0424261df836f089f00764fad2adf4aa0baae89d | C++ | 7,126 | 222 | //===----------------------------------------------------------------------===//
//
// The LLVM Compiler Infrastructure
//
// This file is dual licensed under the MIT and the University of Illinois Open
// Source Licenses. See LICENSE.TXT for details.
//
//===----------------------------------------... |
23527995e30b9a75996820f89fa993bd10f6aaf73d90287304cdc1c3636e0edc | C++ | 7,149 | 395 |
#ifndef _AUXCLASS
#define _AUXCLASS
#ifndef INFINITY
#define INFINITY 1000000000
#endif
//#define INLINE __attribute__ ((always_inline))
#define INLINE inline
//#define __SSE2
class ParamStruct
{
public:
ParamStruct()
{}
REAL Temp;
REAL numit;
REAL gammaDE;
REAL GM_mask;
REAL particle_weight;
RE... |
0a0edbcd2afb71aff756abedfbb8dc7e3a75181660840609129598d038160283 | C++ | 7,162 | 172 | // 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) 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... |
f53485df477c8d04567505f9eb69f1f4d899641027349e018df4c1c86fffc021 | C++ | 7,184 | 203 | // test_duration.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... |
05b704ccb39a712664ac484633c91134c85331f6e0a69fcf656c328b0f602dcf | C++ | 7,228 | 281 | //
// 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
//
//------------------... |
32db78af6820373b792973c99bf7f6e26d665ef1d184092dacf836b9f9f2dff1 | C++ | 7,240 | 255 | //
// reply.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 "reply.hpp"
#include <string>
namespace... |
c1c78770690c82a0d2540d8d33f255c15d6f021c701f806cb5cb0e1c819662aa | C++ | 7,240 | 238 | /***************************************************************************************************************
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... |
11a4a9c285cb73b551b7c7380ecbd5fed31e4e8858b3b0e176c6835eef42f11d | C++ | 7,258 | 295 | /*
*
* 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... |
4b394c95315eaf30a072b8e90c6be1f1a1a487841f95a1de24a2538b24a32e3f | C++ | 7,272 | 208 | #if defined _WIN32 || defined __CYGWIN__
#define DLL_PUBLIC __declspec(dllexport)
#else
#define DLL_PUBLIC __attribute__((visibility("default")))
#endif
#include "Python.h"
#include "numpy/arrayobject.h"
#include "on_demand_object_mesh_generator.h"
#define MODULE_NAME "_neuroglancer"
namespace neuroglancer {
namespac... |
62c8906bb0d12ea84d60217b3773cd8e1768db4aab934880db2316df7026cab8 | C++ | 7,282 | 208 | // 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... |
991db180e1064a9ebfc8e5c100cd1a172087d724e7f2153f628d9e223e9e4fc1 | C++ | 7,292 | 256 | //
// reply.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 "reply.hpp"
#include <string>
#include <... |
ac4cafb6d784f82b171026c7c8cd7a57cc63037d39c0aeef325c2b9c7cdc3824 | C++ | 7,294 | 256 | //
// reply.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 "reply.hpp"
#include <string>
#include <... |
bead98a13ed13ca4c579c67ebd1f2ca296791be4bad48c0167488622b6904859 | C++ | 7,294 | 256 | //
// reply.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 "reply.hpp"
#include <string>
#include <... |
efd6abc706c8fbb609ec5a9ff7f9d8f2b002b40c592a01e5f9cbbb3994ac6a72 | C++ | 7,294 | 256 | //
// reply.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 "reply.hpp"
#include <string>
#include <... |
bef92e1f28b84335a98b54ebfb99564c132f72335d88eb5311bf87d43f7f921b | C++ | 7,303 | 171 | //---------------------------------------------------------------------------//
// 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... |
accca51dfd21023cda8627ef8e736979498d65570512822a067afbe80350db9b | C++ | 7,306 | 244 | // runtime_resolution.cpp ----------------------------------------------------------//
// Copyright 2008 Howard Hinnant
// Copyright 2008 Beman Dawes
// Copyright 2009 Vicente J. Botet Escriba
// Copyright (c) Microsoft Corporation 2014
// Distributed under the Boost Software License, Version 1.0.
// See http... |
d66ca87ad1a76d9510c269822ffb6ac134d15353b8a6d5ae2af2733591d646ae | C++ | 7,323 | 244 | //
// 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... |
82350b3b5c56e0c188c76b1661524b20901f5ac018bfd3c25e43aa6566dd2e97 | C++ | 7,329 | 253 | //---------------------------------------------------------------------------//
// 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... |
a7879250b89a9d668b4749151f98ca58502026197d2cf3066869c3c795c4ef3c | C++ | 7,386 | 194 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2011 Kolja Brix <brix@igpm.rwth-aachen.de>
// Copyright (C) 2011 Andreas Platen <andiplaten@gmx.de>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser Gen... |
84770a2762cd6cf142b7340cface230359344fcc9a3980ceba71aaef0777902d | C++ | 7,388 | 208 | // (C) Copyright Pieter Bastiaan Ober 2014.
// 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)
#include <boost/test/unit_test.hpp>
#include <boost/test/tools/floating_point_compa... |
d99af8573a5f4d2eed3b1591dda48a426f021c2164335bc05ee0137c5a7c82f5 | C++ | 7,395 | 166 | #include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "SequenceFuns.h"
#include "SoloCommon.h"
#include <unordered_map>
#include <bitset>
#include "systemFunctions.h"
void SoloFeature::countVelocyto()
{//velocyto counting gets info from Gene counting
time_t rawTime;
nReadPerCB... |
744bc9102efdf4f68cd0a0f44dd28e71871659623d0ff771b9502255c76f262f | C++ | 7,396 | 163 | #include "ReadAlignChunk.h"
#include "Parameters.h"
#include "OutSJ.h"
#include <limits.h>
#include "ErrorWarning.h"
int compareUint(const void* i1, const void* i2) {//compare uint arrays
uint s1=*( (uint*)i1 );
uint s2=*( (uint*)i2 );
if (s1>s2) {
return 1;
} else if (s1<s2) {
return ... |
ae2bfe2503eb5a0026afc964997cf31fd8dd0c8b1c41307a0d12d7857ee24cc8 | C++ | 7,437 | 204 | #include "udp_server.h"
#include "api_config.h"
#include "socket_utils.h"
#include "stream_info_impl.h"
#include "util/strfuns.hpp"
#include <asio/io_context.hpp>
#include <asio/ip/address.hpp>
#include <asio/ip/address_v4.hpp>
#include <asio/ip/multicast.hpp>
#include <asio/ip/udp.hpp>
#include <exception>
#include <l... |
b81909d0754a8df50699f51c0e7f438eb21b5a889ee56e3674fd03f9a0bc1b64 | C++ | 7,437 | 209 | #include "../common/bytecmp.hpp"
#include "sample.h"
#include "send_buffer.h"
#include "stream_info_impl.h"
#include "tcp_server.h"
#include <asio/read.hpp>
#include <asio/read_until.hpp>
#include <asio/write.hpp>
#include <catch2/catch.hpp>
#include <functional>
#include <sstream>
#include <thread>
// clazy:excludeal... |
6f3a874bd84142343b5f7580d25962b678e1dc8ec66d41f7297801ce42338833 | C++ | 7,453 | 161 | // 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... |
fd57889b9c50d00a6cfce6116331d03628e6ca3633aa9344d224eff6635e9ad6 | C++ | 7,455 | 212 | // (C) Copyright Herve Bronnimann 2004.
// 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)
#include <utility>
#include <functional>
#include <algorithm>
#include <numeric>
#inclu... |
3e896a39f51b159fb60f6d08a7dca0df5c96fd792dabc09c6445b51adf72e3c4 | C++ | 7,456 | 209 | #include "time_receiver.h"
#include "api_config.h"
#include "inlet_connection.h"
#include "socket_utils.h"
#include <limits>
#include <loguru.hpp>
#include <sstream>
/// internally used constant to represent an unassigned time offset
const double NOT_ASSIGNED = std::numeric_limits<double>::max();
using namespace lsl;... |
536a8fe831a31c64d7f15e7a25789304b59df44e6f5dc8b16a2b66e200b92838 | C++ | 7,475 | 290 | #include <boost/asio/execution.hpp>
#include <boost/asio/static_thread_pool.hpp>
#include <algorithm>
#include <condition_variable>
#include <memory>
#include <mutex>
#include <queue>
#include <thread>
#include <numeric>
using boost::asio::static_thread_pool;
namespace execution = boost::asio::execution;
// A fixed-s... |
5fcc6d47826eae6b49467ebe8215309c7e20a40d936a856108ffefae84975e83 | C++ | 7,481 | 330 | //
// bulk_execute.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... |
017695f5dff8a69a42cae504dce4252e790da53f14b4d467c536fbfa4b35da26 | C++ | 7,494 | 209 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 Lesser General Public
// License as published by the Free Software... |
307c9a67b460f8106fcb830b61606a6ae0fdfdcc4bf17ea371db4ea649545a63 | C++ | 7,503 | 212 | // Copyright(c) 2011 - 2018 Thermo Fisher Scientific - LSMS
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy... |
95196a08ac3eb2104d24d6bb86ee3f232f1fe9655a3f1d893f2736ffcf3d3380 | C++ | 7,508 | 246 | //
// 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
//
//------------------... |
65d0eac56adb41bd372a14233f8781fef422a5a09063703108f7ce5c5437abd2 | C++ | 7,531 | 312 | /*
*
* 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... |
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