sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1797225698f0ce551b70e3fc76914cf41aa1e59a721b14bc592a24708d5b0653 | C++ | 11,196 | 241 | #include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "serviceFuns.cpp"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
#include "SoloFeatureTypes.h"
#include<unistd.h> // for get_current_dir
void SoloFeature::outputResults(bool cellFilterYes, string outputPrefixMat)
{
//ma... |
0771fd62dec975a7f12647bfccc5cf9c59f6dd4ee30ae0dec3da00ebf23f851e | C++ | 11,209 | 292 | #include "api_config.h"
#include "common.h"
#include "util/cast.hpp"
#include "util/inireader.hpp"
#include "util/strfuns.hpp"
#include <algorithm>
#include <cstdlib>
#include <exception>
#include <fstream>
#include <loguru.hpp>
#include <mutex>
#include <stdexcept>
using namespace lsl;
/// Substitute the "~" charact... |
ea6f01a0c17fafaf9aa11b7d98a64139734507e9e40950bd7a93abffb9f0afd5 | C++ | 11,222 | 497 | //
// connect.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 ... |
e78db2798a32c3f275c1cca717579977224e25c9e0dadba9541f3d038b8683e6 | C++ | 11,255 | 313 | #include <sys/types.h>
#include <sys/stat.h>
#include "IncludeDefine.h"
#include "Parameters.h"
#include "SequenceFuns.h"
#include "Genome.h"
#include "Chain.h"
#include "ReadAlignChunk.h"
#include "ReadAlign.h"
#include "Stats.h"
#include "genomeGenerate.h"
#include "outputSJ.h"
#include "ThreadControl.h"
#include "G... |
90c3318e0ae6bada4e0107a1cc18db2050c03f6f70f9f77a27ac0ffb1dc63390 | C++ | 11,265 | 284 | /*
* 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_sse2.cpp
*
* This file contains SSE2 implementation of the \c find_address algorithm
... |
b4912da312d1f683c75d88688c00f30c81a8bfe75c15ceb631968e81f390652a | C++ | 11,269 | 343 | // 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 ... |
125b79d296c426265f9291abbc49ac9fc0646ee734c6d39e4bb4ae6ede8d9ace | C++ | 11,288 | 310 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
b89576955282744854fb74b68d609c35b121526dd46a7b2b5c2150fa788d210a | C++ | 11,365 | 371 | //
// 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/vinniefalco/CppCon2018
//
#include "ht... |
c7daff5211028da79b3ca0473dca18ada9197f38e710f72d0493ad3332ce3ec9 | C++ | 11,369 | 360 | // 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... |
f428ffec6d523ba02a823f476ddb67ddb36378d2819c4319ae8287d02144da11 | C++ | 11,398 | 314 | /*
*
* 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.
... |
264ba90b19cd2dcb29d9af74e60062e53759220cd67c8c855fc8a8faa91fc41b | C++ | 11,436 | 469 | //
// 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... |
de82262d64cfc2e71828c320cedd8be08423c65686384574b6a8b4d6bb795975 | C++ | 11,437 | 345 | #include <typeinfo>
#include <iostream>
#include <Eigen/Core>
#include "BenchTimer.h"
using namespace Eigen;
using namespace std;
template<typename T>
EIGEN_DONT_INLINE typename T::Scalar sqsumNorm(const T& v)
{
return v.norm();
}
template<typename T>
EIGEN_DONT_INLINE typename T::Scalar hypotNorm(const T& v)
{
r... |
61d0f28610f4958fb8c506e9d1ade49a44f6d7af41edb10b51aa2a5fbbde97e2 | C++ | 11,445 | 332 | // 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... |
bf53518fa2189f9c7c611af054711f597f5a3f05150c09bca6b00e2e2a397f85 | C++ | 11,455 | 382 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// void_cast.cpp: implementation of run-time casting of void pointers
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompa... |
7c51826fb74659a7053c717610c49a5e4b2c71047a95f3aca65811cbfb0a12bd | C++ | 11,458 | 352 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 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 Soft... |
7fe6ef8bf0aaa24cf4cd07b9c0d6281db92bb298d6168ae45acabb87d800112b | C++ | 11,474 | 332 | // 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... |
c381ad8bd0ef2572d7dd019a657ae55117927cb184c301c732de9b265fe9a49e | C++ | 11,491 | 321 | //---------------------------------------------------------
// Copyright 2018 Ontario Institute for Cancer Research
// Written by Jared Simpson (jared.simpson@oicr.on.ca)
//---------------------------------------------------------
//
// This version modified by Oxford Nanopore Technologies for
// use as a standalone pr... |
928d98fdba3eabe6be51635554bb9aa9cb30e27404c93afc6e00b9da47644c3c | C++ | 11,506 | 206 | /*
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_lvalue_reference.hpp>
#include "tes... |
a33992fe7eb750f0165ba400c2729e23b4424bf8cebe5532c68ec5f43e1537b7 | C++ | 11,515 | 382 | /////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
// void_cast.cpp: implementation of run-time casting of void pointers
// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
// Use, modification and distribution is subject to the Boost Software
// License, Version 1.0. (See accompa... |
97dc00ab86bf3075637ee86d2108bfddfcab305f1782afa07995d03e7b5cf79c | C++ | 11,542 | 356 | //
// 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
//
//------------------... |
a80c0693b8967c1b8c11a0db11c479a285a10417a9bb40306b16c522cc9ebd08 | C++ | 11,542 | 329 | //
// address_v4.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.
... |
dc9964ddb59fa17563975a1173beaff3d0b7452705027840b0c1dc8cfab9cf02 | C++ | 11,585 | 448 | //
// deadline_timer.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... |
e8e11a777bca45c32e733af1aaaf004f216694cac1712f9e6a374ee380442115 | C++ | 11,606 | 460 | /*
MIT License
Copyright (c) 2021 Shifu Chen <chen@haplox.com>
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, modify, m... |
32bc5a7190daa4624dbc4787c9a78a5d581ef5916d36e1819826b5c2884c1418 | C++ | 11,669 | 557 | //
// receiver.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 ... |
965233b8c2d014f1bb55e28c4a97acf0713a32f9c7ec6e21ebca9a85600e92ba | C++ | 11,766 | 438 |
#include "ParticleGrid.cpp"
#include <mex.h>
#include <vector>
#ifdef PARALLEL_OPENMP
#include <omp.h>
#endif
class RJMCMCBase
{
public:
ParticleGrid<Particle> pcontainer;
REAL *vfmap;
REAL *dataimg;
const int *datasz;
EnergyComputerBase *enc;
REAL itmax;
REAL gammaDE;
REAL width;
RE... |
5b34a17b10587696235d8bd046be1cbeabd82bf1f79c7b8378d4c54bb4518cfd | C++ | 11,783 | 302 | #include "api_config.h"
#include "common.h"
#include "util/cast.hpp"
#include "util/inireader.hpp"
#include "util/strfuns.hpp"
#include <algorithm>
#include <cstdlib>
#include <exception>
#include <fstream>
#include <loguru.hpp>
#include <mutex>
#include <stdexcept>
using namespace lsl;
/// Substitute the "~" charact... |
ff2eff4d58d4074f796944da3264bd8e48977ecc427ef0b815cd6e2d13e6a2ad | C++ | 11,841 | 330 | #include "stream_info_impl.h"
#include "api_config.h"
#include "cast.h"
#include <algorithm>
#include <loguru.hpp>
#include <sstream>
namespace lsl {
using namespace pugi;
using lsl::to_string;
stream_info_impl::stream_info_impl()
: channel_count_(0), nominal_srate_(0), channel_format_(cft_undefined), version_(0),
... |
8d5f074755e0e5aacaa763d079020102a178f16d3bf78f2fa9cf347b040e6b9e | C++ | 11,899 | 263 | #include "Parameters.h"
#include "ErrorWarning.h"
void Parameters::samAttributes(){//everything related to SAM attributes
//outSAMattributes
outSAMattrPresent.NH=false;//TODO re-write as class with constructor?
outSAMattrPresent.HI=false;
outSAMattrPresent.AS=false;
outSAMattrPresent.NM=false;
... |
6553a3ebeda538df7327b91730c7d63b3477aecdd77d4e0f95c9d1b87a673f29 | C++ | 11,934 | 257 | /*
* Created by Fahimeh Mirhaj on 5/30/19.
*/
#include "GTF.h"
#include "streamFuns.h"
#include "genomeParametersWrite.h"
void GTF::superTranscript() {
if (P.pGe.gTypeString!="Transcriptome" && P.pGe.gTypeString!="SuperTranscriptome") {
return;
};
//write full genome
mkdir((genome.pGe.g... |
16206079f79854520cdb643db08c880d287d8f1ae0a1ec1a9632422122de7716 | C++ | 11,946 | 313 | #include "inlet_connection.h"
#include "api_config.h"
#include <functional>
#include <loguru.hpp>
#include <sstream>
using namespace lsl;
namespace asio = lslboost::asio;
namespace ip = asio::ip;
inlet_connection::inlet_connection(const stream_info_impl &info, bool recover)
: type_info_(info), host_info_(info), tcp_... |
6fef2f06aa23265304f738ddfd6e89e397af5f1f6040dbc9e69b7acfa8d63894 | C++ | 11,971 | 396 | /*
Copyright Barrett Adair 2016-2021
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 <utility>
#include <boost/callable_traits/is_invocable.hpp>
#include "test.hpp"
#ifde... |
09b67d26d6178c1f9a866cd49ae471e0499a08d72bd4efa9acca10fcf5dfff08 | C++ | 11,986 | 480 | //
// 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
//
//------------------... |
3e33a7568fb181fdad65fce125f818aa18634f5c33a8c44dca45a567ff3b31ff | C++ | 12,020 | 410 | #include "SuffixArrayFuns.h"
#include "PackedArray.h"
inline uint medianUint2(uint a, uint b)
{
// returns (a+b)/2
return a/2 + b/2 + (a%2 + b%2)/2;
};
uint compareSeqToGenome(Genome &mapGen, char** s2, uint S, uint N, uint L, uint iSA, bool dirR, bool& compRes)
{
/* compare s to g, find the maximum ident... |
30ec5822900f49e232ddd86e577cda63dfdbb1cecc61205a0d8dac31239d3273 | C++ | 12,040 | 319 | /*
* inserts sequences into the SA
* returns number of SA indexes inserted
*/
#include "insertSeqSA.h"
#include "ErrorWarning.h"
#include "SuffixArrayFuns.h"
#include "SequenceFuns.h"
#include "serviceFuns.cpp"
#include "streamFuns.h"
#include "binarySearch2.h"
#include "funCompareUintAndSuffixes.h"
#include "funCom... |
3e6d368e6e2403e46a64a33d5f117252738c0028caf3a925f8001ebdcc12d964 | C++ | 12,072 | 433 | //
// 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 <algorithm>
#include <cstdlib>
#includ... |
d60f1cd989a9a55e57a299dfb7bec61d47a1df78433ab07fbd297ceb71e2cee2 | C++ | 12,096 | 317 | // Copyright 2011 Vicente J. Botet Escriba
// Copyright (c) Microsoft Corporation 2014
// Distributed under the Boost Software License, Version 1.0.
// See http://www.boost.org/LICENSE_1_0.txt
#include <boost/chrono/chrono_io.hpp>
#include <sstream>
#include <boost/detail/lightweight_test.hpp>
#include <boost/chro... |
e37a2882af4f71645c81f78c94d6804b34793a24efda6807c0d859038b7ef91a | C++ | 12,180 | 387 | //
// 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
//
//------------------... |
941da22e0903a76137f81881adc0afe88aa7e0524d4c56188713c7ee34a498c0 | C++ | 12,183 | 507 | /*
Multi-precision real number class. C++ interface fo MPFR library.
Project homepage: http://www.holoborodko.com/pavel/
Contact e-mail: pavel@holoborodko.com
Copyright (c) 2008-2010 Pavel Holoborodko
Core Developers:
Pavel Holoborodko, Dmitriy Gubanov, Konstantin Holoborodko.
Contributors:
Br... |
8cb44befc6b019ff71d91bded33db91e48229fe43e410e44dc7bc17f35d3d684 | C++ | 12,229 | 278 | #include <cmath>
#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"
#include "stitchAlignToTranscript.h"
#include "extendAlign.h"
#include "binarySearch2.h"
#include "ErrorWarning.h"
void ReadAlign::stitchWindowSeeds (uint iW, uint iWrec, bool *WAexcl, char *R) {//stitch... |
b977304798cc54dea5a4979c31841025e0f25456ee9bd48498bd414d45c08976 | C++ | 12,303 | 369 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
447a9dfe2ccccffc48a90ced90198962756c077164321c5122548a6649be0bcb | C++ | 12,358 | 267 | #include "Transcriptome.h"
#include "ReadAlign.h"
#include "serviceFuns.cpp"
#include "AlignVsTranscript.h"
#include "ReadAnnotations.h"
#include <bitset>
int alignToTranscript(Transcript &aG, uint64 trS1, uint16 exN1, uint32 *exSE1, uint32 *exLenCum1, array<uint32,2> &distTrEnds)
{
bool alignIntronic =f... |
caa505fb83777054769be1e375b0d07df440f1b0c0cdb22679ad44a21e5c4267 | C++ | 12,438 | 306 | // 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... |
093cf6599b1e93d6f212b7bc823335558c89a0de12e718521a716097f5f35ebb | C++ | 12,443 | 562 | //
// submit.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... |
32d85312e9044fc10d3015bc7b478bc535eeb9bd779c904e3e9fbc58610c2f35 | C++ | 12,482 | 276 | #include "SoloReadFeature.h"
#include "serviceFuns.cpp"
#include "SequenceFuns.h"
#include "ReadAnnotations.h"
#include "SoloReadBarcode.h"
class ReadSoloFeatures {
public:
uint32 gene;
vector<uint32> geneMult;
vector<array<uint64,2>> sj;
bool sjAnnot;
uint32 indAnnotTr; //index of the annotated tr... |
75036dbd75dc2b071dd1909f50459ac31954cf1df08810afead990a7763f2452 | C++ | 12,505 | 363 | //
// multicast.cpp
// ~~~~~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#i... |
5325c9268fd744f2c476b36038a87d320c0123e2cace9c6f009e40d6a34f06ba | C++ | 12,575 | 285 | /*
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... |
ecb7fb743f4ba086871d0fdd8701d9e0a09fe8b66ebda8bee4e88477d00e39c8 | C++ | 12,650 | 315 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
bc98d59178a9680432e2696e05445865f737fa916fcdcd4c99581de599fcb67f | C++ | 12,686 | 494 |
/* INCLUDING HEADER FILES */
#include "csv_parser/csv_parser.hpp"
/* BEGIN DEFINITION FOR PUBLIC METHODS */
bool csv_parser::init(FILE * input_file_pointer)
{
input_fp = input_file_pointer;
if (input_fp == NULL)
{
fprintf(stderr, "Fatal error : unable to open input file from file pointer\n");
return false;
... |
78803454653d70d73819e06903dd76a761b41507f23ee6cd1e72182d5befe5c3 | C++ | 12,703 | 411 | //---------------------------------------------------------------------------//
// 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... |
e0de7c1b63b25f1bbd69747b0f2e3673626da52b5e70ae9b4230d89adbe60520 | C++ | 12,776 | 335 | #include "inlet_connection.h"
#include "api_config.h"
#include "resolver_impl.h"
#include <asio/io_context.hpp>
#include <asio/ip/address.hpp>
#include <asio/ip/basic_resolver.hpp>
#include <chrono>
#include <exception>
#include <functional>
#include <loguru.hpp>
#include <sstream>
#include <stdexcept>
#include <vector... |
b2b7874fe74dad8557d28ca0950c810d2f352d2863fc3567e22e36de8369c2f2 | C++ | 12,803 | 360 | #include "stream_info_impl.h"
#include "api_config.h"
#include "util/cast.hpp"
#include "util/uuid.hpp"
#include <algorithm>
#include <cstdlib>
#include <exception>
#include <loguru.hpp>
#include <sstream>
#include <stdexcept>
#include <vector>
#include <utility>
namespace lsl {
using namespace pugi;
using lsl::to_st... |
3b0807d1543e0a10cda68cfff9d19849e157048d4976191cd1e44b7efa96c12e | C++ | 12,807 | 324 | #include "Genome.h"
#include "SequenceFuns.h"
#include "streamFuns.h"
#include "ErrorWarning.h"
#include "serviceFuns.cpp"
#include "GTF.h"
#include "funPrimaryAlignMark.h"
template <typename T>
void appendVector(vector<T> &v1, const vector<T> &v2)
{
v1.reserve(v1.size()+v2.size());
v1.insert(v1.end(), v2.begi... |
e28bc395a287def4a9ceadf53bbc30d9fde09fa506d7a56cc60df106cadd18dc | C++ | 12,812 | 454 | #include "stream.h"
#include <iostream>
#include "exp.h"
#ifndef YAML_PREFETCH_SIZE
#define YAML_PREFETCH_SIZE 2048
#endif
#define S_ARRAY_SIZE( A ) (sizeof(A)/sizeof(*(A)))
#define S_ARRAY_END( A ) ((A) + S_ARRAY_SIZE(A))
#define CP_REPLACEMENT_CHARACTER (0xFFFD)
namespace YAML
{
enum UtfIntroState {
uis_start,... |
702995b14cbb108367283239a43ed44660aff12bb3854a8582cc593dbf2f9ffb | C++ | 12,854 | 454 | /**
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include <iomanip>
#include <iostream>
#include <queue>
#include <stdexcept>
#include "args.h"
#include "autotun... |
fb9bf5ca3602ec29d963522933024d8add0b033553163936bdfcd181a0eef74a | C++ | 12,867 | 433 | //
// 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 <algorithm>
#include <cstdlib>
#includ... |
4b660850db2eeadf0294680110a3915a31de7df1716bd548c23e6006b2e09d7d | C++ | 12,896 | 342 | /*
Copyright Barrett Adair 2016-2021
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 <utility>
#include <boost/callable_traits/is_invocable.hpp>
#include "test.hpp"
#ifde... |
1e630e67a80eff98eaccd7cdd870baab4eb16721ff0ff0d6bff744f0ba193c1d | C++ | 12,947 | 360 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2009 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 o... |
81f806d37757bfd124158d5011b0ee2eeeb0bcec53e0f2a9c0b541beb801c45c | C++ | 13,008 | 435 | //
// 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 ... |
ed6fdac2fa00b82e917e57ec5cc3aeebf779d1d4e6283da905a0fc2474828fe2 | C++ | 13,013 | 355 | //---------------------------------------------------------------------------//
// Copyright (c) 2014 Benoit Dequidt <benoit.dequidt@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://boo... |
c46fe04e47192bc2792565830378a130b0a412539c8b1d204cb7355286a74fd3 | C++ | 13,052 | 368 | #include "ReadAlign.h"
#include "SequenceFuns.h"
void ReadAlign::peOverlapMergeMap() {
if (!P.peOverlap.yes || P.readNmates!=2 ) {//no peOverlap //not readNends: this is alignment
peOv.yes=false;
return;
};
//debug
//cout << ">" << readName+1;
//merge PE mates into SE
peMerg... |
fc9a0feca57afd9de90dd450f9d2e5f0addb3de0c2aa630c1d3560e20e83db0e | C++ | 13,097 | 476 | //
// strand.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... |
06e3a427c8b504ef9be59435f00b80c79865aec91a4bd89f9c2f6d233d74a652 | C++ | 13,227 | 343 | // 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... |
143ed058e476113cb353431e006f63b31180f5c33f74b885f7eb18d041b06a5e | C++ | 13,232 | 437 | //////////////////////////////////////////////////////////////////////////////
// Example illustrating the use of GCoptimization.cpp
//
/////////////////////////////////////////////////////////////////////////////
//
// Optimization problem:
// is a set of sites (pixels) of width 10 and hight 5. Thus number of pixels... |
1e050eba0686aa88c5ea1d992c529215a22c07eae62d8f9d184a602ea4621588 | C++ | 13,264 | 333 | #include "sjdbBuildIndex.h"
// #include "sjdbLoadFromStream.h"
// #include "sjdbPrepare.h"
#include "ErrorWarning.h"
#include "SuffixArrayFuns.h"
#include "SequenceFuns.h"
#include "serviceFuns.cpp"
#include "IncludeDefine.h"
#include "streamFuns.h"
#include "binarySearch2.h"
#include "ErrorWarning.h"
#include <cmath>
... |
49c3c823a40169ad0e9872a75dd69a4a169400302b9c7b8667a813d5a41955fb | C++ | 13,293 | 420 | #define BOOST_MATH_DISABLE_STD_FPCLASSIFY
#include "sample.h"
#include "portable_archive/portable_iarchive.hpp"
#include "portable_archive/portable_oarchive.hpp"
using namespace lsl;
sample::~sample() noexcept{
if (format_ != cft_string) return;
for (std::string *p = (std::string *)&data_, *e = p + num_channels_; p... |
3680fca8e53d4c8759cedac0b556e79b73fdbe4dd57909e62c6cbdbd90b3fb5e | C++ | 13,405 | 321 | // 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... |
235541818419351da8420c72f668e5c78873b9c3dae974702849adc582c06d7c | C++ | 13,444 | 340 | //
// composed_6.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... |
8cdd67ed0b13c192c11e5ea90e9d5782d6627eb303fbc4aa5ebda2531ec00ff8 | C++ | 13,447 | 479 | /*
* A C++ I/O streams interface to the zlib gz* functions
*
* by Ludwig Schwardt <schwardt@sun.ac.za>
* original version by Kevin Ruland <kevin@rodin.wustl.edu>
*
* This version is standard-compliant and compatible with gcc 3.x.
*/
#include "zfstream.h"
#include <cstring> // for strcpy, strcat, strlen... |
3fa7a458e163cc4e3865f6d06d080066e154194d2ada2338a3fd851f233a1dda | C++ | 13,448 | 376 | #include "../src/cancellable_streambuf.h"
#include <asio/io_context.hpp>
#include <asio/ip/multicast.hpp>
#include <asio/ip/tcp.hpp>
#include <asio/ip/udp.hpp>
#include <asio/ip/v6_only.hpp>
#include <asio/read.hpp>
#include <asio/use_future.hpp>
#include <asio/write.hpp>
#include <catch2/catch.hpp>
#include <chrono>
#... |
bc97b33293a61a60146186286c0db8c36af58af3576657b97dc36464ae4ef611 | C++ | 13,486 | 405 | /***************************************************************************************************************
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... |
9f904b16ac586c890c0dbb78a893cc6fdd7b608c2e6dc1314b02100b0f27f4bb | C++ | 13,532 | 420 | /*
Copyright (c) T. Zachary Laine 2018.
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/algorithm/find_backward.hpp>
... |
572c4bd4e8f068454c2ab59afdb8081fe6a7c8362e3dd0240ebddbf624951b83 | C++ | 13,565 | 365 | // 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 ... |
18a230edf29f40eef9f45f56c293c8bc23639bc9e51809a960ee733a75c0983d | C++ | 13,615 | 525 | //
// system_timer.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... |
17261fdd6082505f0f95cda7e1ff37656f88c87c2dda82555d54fddd3bb74ea6 | C++ | 13,630 | 345 | //
// composed_6.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... |
bb40a734062b551c472770b4037b54c0a633a9c95d0758ad3520abb8468b4c81 | C++ | 13,631 | 639 | /***************************************************************************************************************
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... |
6332a05da9e53de3c61f4b0f9a360c6fdb9feac866c6006deeb1a1ceae4095f7 | C++ | 13,655 | 446 | //
// Copyright (c) 2016-2019 Vinnie Falco (vinnie dot falco at gmail dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Official repository: https://github.com/boostorg/beast
//
#include "snippets.h... |
b27da018e02e4991a2421baba7bfa0561944f3234a62ae99aa8d93248361d9ec | C++ | 13,674 | 505 | // saturating.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 ex... |
5fbe79e5fa3018a0478107ce781a56e3847af29b0e71ec1fcaec420421ccb9d0 | C++ | 13,733 | 525 | /*
* sparsefa.cpp
* peer
*
* Created by Oliver Stegle on 3/25/11.
* Copyright 2011 __MyCompanyName__. All rights reserved.
*
*/
/* TODOs
setter and getter for sigma off
*/
#include "sparsefa.h"
#include "sparsefa.h"
#include "bayesnet.h"
using namespace Eigen;
using namespace std;
using namespace... |
f343715a20efa0394f55a8fa8f8b7f63dd7248ab23f2dddd87969d7991e9e146 | C++ | 13,761 | 485 |
//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... |
1a5e9d4c5457c76660592288352a1117452e8ec32ca3406f58f3ab5499a421cf | C++ | 13,781 | 349 | //
// composed_6.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... |
f1ef03070a3b67972ae8871e7859d3e7f6fabf0e92200c8f64cafd7d62feabd9 | C++ | 13,879 | 477 | /**
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include "autotune.h"
#include <algorithm>
#include <csignal>
#include <functional>
#include <iomanip>
#include... |
c34b9fb0705be6ed2517c921e2513e508cc5b29d7f180d9f0c3534034e8de307 | C++ | 13,936 | 350 | #include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"
#include "SequenceFuns.h"
#include "stitchWindowAligns.h"
#include "sjAlignSplit.h"
#include "PackedArray.h"
#include "GlobalVariables.h"
#include <time.h>
void ReadAlign::stitchPieces(char **R, uint Lread) {
//zero-... |
5cb8573dc77b3d90144804e55d25aeebda2b3e651b6b2571dd1966cbfd4038da | C++ | 13,966 | 410 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2011 Gael Guennebaud <gael.guennebaud@inria.fr>
// 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 ... |
01807f327d1dbfc790e63a02f7780a9c4f3dc1e171c0fec01a0fc025e0cebfda | C++ | 14,033 | 432 | //
// 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
//
//------------------... |
0aaf72c4c884633df0f4059fba250799fdbd3f2f174f9c9b53bf845c159308bd | C++ | 14,081 | 312 | #include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"
#include "blocksOverlap.h"
bool ReadAlign::chimericDetectionOld() {
//////////////////// chimeras
//stich windows => chimeras
//stich only the best window with one of the lower score ones for now - do not sti... |
73467f07bb8bc24003fd23bef09b7504c0bfbb8897ae0a6e4666456c374d558d | C++ | 14,151 | 512 | #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... |
7c9504536ab07300a764ae283d0975595b43c8b88098f2e7c0e39e4d3b796c54 | C++ | 14,206 | 393 | #include "mex.h"
#include "cokus.cpp"
// Syntax
// [ WP , DP , Z , X ] = GibbsSamplerSWLDA( WS , DS , T , N , ALPHA , BETA , GAMMA0, GAMMA1, SEED , OUTPUT , ZIN , XIN )
// The Special Words (SW) model
void GibbsSampler( double ALPHA, double BETA, double GAMMA0, double GAMMA1, int W, int T, int D, int NN,... |
8b5ef34b24a05cba67634d57561a5d709c3c4ace8e89e016d1651cff70aefbdd | C++ | 14,215 | 380 | // 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 ... |
7d0ee0a9256d5f88503dd29c1338133ddabc775cd9e2aa20c0d86f835dea3d35 | C++ | 14,248 | 210 | #include "legacy_abi.h"
#include "../common.h"
#include "../resolver_impl.h"
#include "../stream_info_impl.h"
#include "../stream_inlet_impl.h"
#include "../stream_outlet_impl.h"
#include <pugixml.hpp>
#include <sstream>
#define NO_EXPLICIT_TEMPLATE_INSTANTIATION
using namespace lsl;
using namespace pugi;
// === Im... |
a20eb7d115a80ca7333a5d456f94039b1e331dc27b627e81a73da492b157eb17 | C++ | 14,295 | 554 | //
// compose.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... |
9b0dcb17490feea51e96bbe9eac99943fda40fe04d703e1ac81343a46b59e143 | C++ | 14,323 | 445 | #include "SequenceFuns.h"
#include <assert.h>
void complementSeqNumbers(char* ReadsIn, char* ReadsOut, uint Lread) {//complement the numeric sequences
for (uint jj=0;jj<Lread;jj++) {
switch (int(ReadsIn[jj])){
case (3): ReadsOut[jj]=char(0);break;
case (2): ReadsOut[jj]=char(1);br... |
c68d24ef510bda278a96167631b44004c90b5e113ac1dfeded1e8175e8c84b9c | C++ | 14,357 | 453 | //
// 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)
//
// Test that header file is self-contained.
#include <boost/beast/core/detail/var... |
b671072ad970e7fba4016c6b3ec426dfb5c4950bb1b61b4a5454398bad17ad9d | C++ | 14,444 | 328 | // (C) Copyright Jesse Williamson 2009
// 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 <iostream>
#include <vector>
#include <boost/config.hpp>
#include <boost/algor... |
f817b860228ca23eaf46471bdf38a708b7d9032ee2d9b2ccbf89cfdfd4f65522 | C++ | 14,552 | 396 | //---------------------------------------------------------------------------//
// 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... |
b11673285edd158300b32ee77b20cea9890dcb4665a5c42e615113c4c35ae313 | C++ | 14,615 | 359 | #include "ReadAlign.h"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
uint ReadAlign::outputTranscriptSAM(Transcript const &trOut, uint nTrOut, uint iTrOut, uint mateChr, uint mateStart, char mateStrand, int unmapType, bool *mateMap, ostream *outStream) {
if (P.outSAMmode=="None") return 0; //no SAM output
... |
472382ccb3786543f98c84ddace91cf4d5bb3db66009b2e78de19978dfbe3587 | C++ | 14,619 | 438 | //
// 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 ... |
affba796af7ba12666046be631b31b9b1b0b941dd35cc92569063867f35fe109 | C++ | 14,656 | 491 | //
// 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
//
//------------------... |
993bf1445a2fb03a0181882c83d2e1cd6481c8c20f83b611e2453d6c53390df2 | C++ | 14,784 | 327 |
#include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "SequenceFuns.h"
#include "SoloCommon.h"
#include <unordered_map>
#include <bitset>
#include "serviceFuns.cpp"
#include <math.h> /* log */
void SoloFeature::quantTranscript()
{//velocyto counting gets info from Gene counting
... |
63484798a07b9d15ccc1bc74816e66f09958c281700fcaccaaba45b5151e1aea | C++ | 14,818 | 358 | #include "data_receiver.h"
#include "api_config.h"
#include "cancellable_streambuf.h"
#include "inlet_connection.h"
#include "sample.h"
#include "socket_utils.h"
#include "util/cast.hpp"
#include "util/endian.hpp"
#include "util/strfuns.hpp"
#include <chrono>
#include <exception>
#include <iostream>
#include <loguru.hp... |
5a9c9c5ce2b1fbc30bd536479bc663579cbd618974c25559a79820f82c27f5a9 | C++ | 14,901 | 356 | #include "data_receiver.h"
#include "api_config.h"
#include "cancellable_streambuf.h"
#include "cast.h"
#include "inlet_connection.h"
#include "sample.h"
#include "socket_utils.h"
#include <iostream>
#include <loguru.hpp>
#include <memory>
#include <sstream>
// a convention that applies when including portable_oarchiv... |
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