sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
164bc33ddca4d8cb5057d33b1050a4b1ee6af9eb62359308e296feea9d8cdfe8 | C++ | 27,750 | 614 | #include "ReadAlign.h"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
#include "IncludeDefine.h"
# include "BAMfunctions.h"
#include <type_traits>
void ReadAlign::samAttrNM_MD (Transcript const &trOut, uint iEx1, uint iEx2, uint &tagNM, string &tagMD) {
tagNM=0;
tagMD="";
char* R=Read1[trOut.roStr==0... |
919b71e39a58f77b7fbe08a1e33379c25d12d5a67e68af26a18a1a49e40b7c64 | C++ | 28,102 | 823 | #include "tests.h"
#include "yaml.h"
namespace Test
{
namespace Emitter {
////////////////////////////////////////////////////////////////////////////////////////////////////////
// correct emitting
void SimpleScalar(YAML::Emitter& out, std::string& desiredOutput) {
out << "Hello, World!";
desiredOutput ... |
d2cfbafa3bc933b55b3b2cb55860811c65a0b9863e2290958aae920bda6be295 | C++ | 28,564 | 658 | #include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "serviceFuns.cpp"
#include <unordered_map>
#include "SoloCommon.h"
inline int funCompareSolo1 (const void *a, const void *b); //defined below
inline int funCompare_uint32_1_2_0 (const void *a, const void *b);
void SoloFeatur... |
a33a9b2d1ca0977f7dae4850e0408bcf5966d445e0272e987fe18efdbd33202e | C++ | 28,689 | 702 | //
// Created by Till Konrad Aust on 17.12.21.
//
// in case of simulation set flag
#define SIMULATION
#define MIN_TIME_BETWEEN_MSG 1
#include "kilogrid_stub.h"
/*-----------------------------------------------------------------------------------------------*/
/* Initialization of the Loopfunctions. ... |
77f7f6006c5c91dd84676b34c9b800240ed47ebba5f4502dab38f3902d32909a | C++ | 28,787 | 878 | //
// buffer.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... |
4db3f6f3c2c0a5dfc3863394fe1a50afc711952704c8af889e8d014493c11897 | C++ | 29,195 | 1,019 | #include <Rcpp.h>
#ifdef __EMSCRIPTEN__
#define __linux
#include <Rcpp/Benchmark/Timer.h>
#undef __linux
#else
#include <Rcpp/Benchmark/Timer.h>
#endif
#include <deque>
#include <cmath>
using namespace Rcpp;
// Exported convenience functions ---------------------------------------------
//' Euclidean distance between... |
f589c9c040d090bd3b28a1f4f2615ae320f7901502646328462aacfdc45929f8 | C++ | 29,349 | 522 | #include <stdio.h>
#include "fastqreader.h"
#include "unittest.h"
#include <time.h>
#include "cmdline.h"
#include <sstream>
#include "util.h"
#include "options.h"
#include "processor.h"
#include "evaluator.h"
// TODO: code refactoring to remove these global variables
string command;
mutex logmtx;
int main(int argc, c... |
8d03fe2e69f5ecbb97576cb760d91ac15453a514bc9e69ddc442a58cfd2fb384 | C++ | 29,426 | 1,030 | //
// 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
//
//------------------... |
d9752965e253cff79e759ad81991a0aaa57b640892307c0f3496e1ecf256de70 | C++ | 29,426 | 426 | // Predictive-coding-inspired Variational RNN
// error_regression.cpp
// Copyright © 2022 Hayato Idei. All rights reserved.
//
#include "network.hpp"
#include <sys/time.h>
#include <opencv2/opencv.hpp>
//hyper-parameter used in error regression
#define TEST_SEQ_NUM 6 //sequence number of target data in error regress... |
c2f2c4559a5392b059b1b1fcd702f66d343f22deccb30fecf4e44205c110c066 | C++ | 29,505 | 900 | #include<stdio.h>
#include<string>
#include<stdlib.h>
#include<math.h>
using namespace std;
# define gr (double)1.0
# define eps (double)0.05
void sol_0(double t0, double t, double *x0, double *x, double *para, double *para2);
void sol_1(double t0, double t, double *x0, double *x, double *para, double *para2);
void... |
13b54407c457defb79907466810d464109b5eae0df30beab3a2390a82dffee99 | C++ | 29,646 | 839 | //
// 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 ... |
b321bb18bb7e290e90fb82ddad84803a3bab53b4a54b8ceaee2f33d65c27354b | C++ | 30,128 | 692 | /*
*
* 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.
... |
59f32a2fd599d399b5daab7a2044f2e0a0262ff533deda31fc0d67355f1b1cdd | C++ | 30,423 | 808 | /*
*
* Old compiling notes:
* --------------------
* mex sdk_mex.cpp ADIDatIOWin.lib
* mex -v sdk_mex.cpp LoadADIDatDll.cpp ADIDatIOWin64.lib
*
* Compiling should be done via:
* adi.sdk.makeMex()
*
* http://www.mathworks.com/help/matlab/matlab_external/passing-argu... |
f18d30e769113fbcaa5ce29978b289fd275e0efc532588ac81bcb32564cc41a9 | C++ | 31,003 | 982 | #include "stats.h"
#include <memory.h>
#include <sstream>
#include "util.h"
#define KMER_LEN 5
Stats::Stats(Options* opt, bool isRead2, int guessedCycles, int bufferMargin){
mOptions = opt;
mIsRead2 = isRead2;
mReads = 0;
mLengthSum = 0;
mEvaluatedSeqLen = mOptions->seqLen1;
if(mIsRead2)
... |
2c3364cdbcc6ed42fbd474418f01016bc2d3d637102bcdec4191abaff3041ba7 | C++ | 31,183 | 1,087 | //
// 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 ... |
fea9a5671b7492efbe3746f0f35d59b83b49ee44d94da9fc1f4db80e1a79b201 | C++ | 32,018 | 1,020 | // 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 ... |
88a05b6d1e01fbc0b29e23352c9d754815125668239c3cd2d271ea1e59564be7 | C++ | 32,258 | 866 | // 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 ... |
cfd598b6c0f72f6ac31f733dfc875c841026b54695e705a605c923e3197188c9 | C++ | 33,514 | 973 | // 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)
// (C) Copyright 2007 Anthony Williams
// (C) Copyright 2007 David Deakins
// (C) Copyright 2011-2018 Vicente J. Botet Escriba
//#define BOOST_THREAD_VERSION 3
#i... |
071c52f84050ed13b52fc45e08bedd4e20bef905634db586bd05d3213e2b9ceb | C++ | 35,447 | 1,143 | // 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 ... |
a08f59600248dbc22a593ecf19ddab5429f6432d7da5d2b7750896d3390ef1c4 | C++ | 37,379 | 721 | #include "ParametersSolo.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include "SequenceFuns.h"
#include "serviceFuns.cpp"
#include <stdlib.h>
void ParametersSolo::initialize(Parameters *pPin)
{
pP=pPin;
cellFiltering();
if (pP->runMode=="soloCellFiltering") {//only filter... |
1add2f445fe954fe07802c39ea8ed90f5a63404f4b4e884bbafc028d816a667b | C++ | 37,408 | 1,420 | //
// 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 ... |
be9df1661c524445b0da89a508b10897f545c7288e0fc12b25d4f050ed6bbb59 | C++ | 37,675 | 1,097 | //
// 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 ... |
ba7346672cf60a04429409a8f06578636106428445719dd1066a576617549a06 | C++ | 38,240 | 1,255 | // 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 ... |
239cbfac9f185223e3208487db008c9e28615a45cefa6d0d0e820e90fa39eeaf | C++ | 39,014 | 1,222 | // 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 ... |
9ad12cad1f1a517a9b13c981aa9b89f97b672180e94487b2600ee72f2e63f5b2 | C++ | 39,220 | 1,190 | //
// 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 !d... |
65f3c5f3b81f3d14420ec1af6f7332e1722dfa4a9c1d42e8b8f88d4f277fdb1c | C++ | 39,582 | 1,177 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
a9e2a21b25d3e8264a3604542a593120d18442bdafd37aa9133e91d4354eed69 | C++ | 39,777 | 709 | // Predictive-coding-inspired Variational RNN
// learning.cpp
// Copyright © 2022 Hayato Idei. All rights reserved.
//
#include "network.hpp"
#include <sys/time.h>
#include <opencv2/opencv.hpp>
//hyper-parameter for learning
#define EPOCH 100000 // iteration of parameter update in training (set in the main function ... |
2c82bc6b78d2d52b945da330749516390686992b95a413d682a1aafbf428e261 | C++ | 40,045 | 1,233 | /* ========================================================================= *
* *
* OpenMesh *
* Copyright (c) 2001-2015, RWTH-Aachen University *
* ... |
58a6181802860051bbffbc40aff9bb5d5ae5abc27dea6426ae691b1850399840 | C++ | 41,168 | 1,090 | #include "peprocessor.h"
#include "fastqreader.h"
#include <iostream>
#include <unistd.h>
#include <functional>
#include <thread>
#include <chrono>
#include <memory.h>
#include "util.h"
#include "adaptertrimmer.h"
#include "basecorrector.h"
#include "jsonreporter.h"
#include "htmlreporter.h"
#include "polyx.h"
PairEnd... |
ade44c071509808260c1ed327874ac96fd9af083c48b13c412eb63859e53b77f | C++ | 41,628 | 1,380 | //---------------------------------------------------------------------------//
// Copyright (c) 2016 Jakub Szuppe <j.szuppe@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... |
29975205f1b2c55d9dfac61fc730544e36bff597454d824052fee3df9348774a | C++ | 41,945 | 1,481 | //
// 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 ... |
98cf1ecc502a80a01544bf95927635868d015db49fe52edddd75255ef4cc0059 | C++ | 43,421 | 1,351 | //
// tcp.cpp
// ~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#if !defined(B... |
c6815befefa250b9c93fe33e1282ef2f390799cec15042fa5ea93c39ba7fa487 | C++ | 44,039 | 1,052 | //
// 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 ... |
06354506fd011a3a545f1f726bcc9fa075ed7f929c7153bce2b1f13c8a23baf5 | C++ | 45,399 | 1,192 | // 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 ... |
539f11f4d74a8e912cdb4059725d4c8d2dbe10e6deff7b49b1754adc95b36cd5 | C++ | 47,098 | 1,414 | /*
* 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) 2011 Helge Bahmann
* Copyright (c) 2013-2014, 2020 Andrey Semashev
*/
/*!
* \file lock_pool.cpp
*
* This file contains implementation ... |
8bec7f71f1d7101ca9cd8f84f2fa7b5df9dcb0798788a62554c49760dac19f21 | C++ | 48,747 | 1,660 | //
// read_until.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.
... |
a797677e45c1d74ed8006f7c404d66fb8b233f693a358e74de7ed306459daa0c | C++ | 52,032 | 1,272 | //
// relationship.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... |
a08a19c07411cbf1521d082408aaa6d5f07ab9c46cc69a19f34363082997f349 | C++ | 52,088 | 1,272 | //
// outstanding_work.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 ... |
91ca672b8121db18d29120b5976b21d131c75988d097c3f58c70d00da38dabac | C++ | 53,090 | 1,566 | #include<stdio.h>
#include<string>
#include<stdlib.h>
#include<math.h>
using namespace std;
# define gr (double)1.0
void sol_0(double t0, double t, double *x0, double *x, double *para, double *para2);
void sol_1(double t0, double t, double *x0, double *x, double *para, double *para2);
void compute_crossing_time_Q(i... |
4eed28720dd3f37a90f123c0b4a2f306107fb5af99b1ac697a4d892312278303 | C++ | 53,294 | 1,171 | /*
bgmg - tool to calculate log likelihood of BGMG and UGMG mixture models
Copyright (C) 2018 Oleksandr Frei
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License... |
d6f587d37be2739e971579ac736034f16bc9fd7b62c4fd1b7d8f8b6d38a6759b | C++ | 53,949 | 1,655 | // time2_demo.cpp ----------------------------------------------------------//
// Copyright 2008 Howard Hinnant
// Copyright 2008 Beman Dawes
// Distributed under the Boost Software License, Version 1.0.
// See http://www.boost.org/LICENSE_1_0.txt
/*
This code was derived by Beman Dawes from Howard Hinnant's ... |
16cb9ea35860137edb6b2d059c4ad8e1f80b3e43fd65d2135515d7ffb6a570ab | C++ | 54,399 | 1,333 | //
// blocking_adaptation.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 autolinkin... |
756417ef6ddd0014e24757a9516aed09a982125b561874702fafd68c667a8b53 | C++ | 57,206 | 2,166 | #include "spectests.h"
#include "yaml.h"
#include <fstream>
#include <sstream>
#include <vector>
#include <iostream>
namespace {
struct TEST {
TEST(): ok(false) {}
TEST(bool ok_): ok(ok_) {}
TEST(const char *error_): ok(false), error(error_) {}
bool ok;
std::string error;
};
}
#define YAML_ASSERT(cond)... |
24afa1e9778c08b98c8c91fc817960c862b2affffabc0da7b63936da04caf188 | C++ | 59,569 | 1,965 | #ifndef _WIN32
// Disable all warnings from gcc/clang:
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wpragmas"
#pragma GCC diagnostic ignored "-Wc++98-compat"
#pragma GCC diagnostic ignored "-Wc++98-compat-pedantic"
#pragma GCC diagnostic ignored "-Wexit-time-destructors"
#pragma GCC diagnostic ignored ... |
f0d9f421cc6a6ecd539fae0417adf6f80b8ca652dd3563af4cc4366f7240cf53 | C++ | 59,877 | 1,574 | //
// 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 ... |
fbda3d24bb6a31d7d84086e2b98e63de785d1be8a357e35230f8f66576f03df6 | C++ | 60,474 | 2,007 | #if defined(__GNUC__) || defined(__clang__)
// Disable all warnings from gcc/clang:
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wpragmas"
#pragma GCC diagnostic ignored "-Wc++98-compat"
#pragma GCC diagnostic ignored "-Wc++98-compat-pedantic"
#pragma GCC diagnostic ignored "-Wexit-time-destructors"
#p... |
f0562feb570f936d155c3b3618635018e2c646c33d987c00d2933b25f9976dbc | C++ | 61,518 | 1,877 | #ifdef MATLAB_MEX_FILE
#include <mex.h>
#endif
#include "GCoptimization.h"
#include "LinkedBlockList.h"
#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <algorithm>
// will leave this one just for the laughs :)
//#define olga_assert(expr) assert(!(expr))
// Choose reasonably high-precisi... |
bb4eb04d005e3eadc1148f83820444dccc00004751e80004c5584e108361431f | C++ | 65,196 | 1,861 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Thomas Capricelli <orzel@freehackers.org>
#include <stdio.h>
#include "main.h"
#include <unsupported/Eigen/NonLinearOptimization>
// This disables some useless Warnings on MSVC.
// It is intended to be d... |
87abdb0d848bf4466474082080cf6772b332744663197274070838e7d4bc88df | C++ | 69,992 | 1,568 | #include <algorithm>
#include <cassert>
#include <climits>
#include <cstdio>
#include <limits>
#include <vector>
extern "C" {
#define SIMDE_ENABLE_NATIVE_ALIASES
#include <simde_avx2.h> // AVX2 and lower
}
#include "opal.h"
// I define aliases for SSE intrinsics, so they can be used in code not depending on SSE gen... |
0922eeb5f6a7b3738ec2ff516aff208418e13337fd9eec31abbd17d9f43be923 | C++ | 71,642 | 1,417 | /*
bgmg - tool to calculate log likelihood of BGMG and UGMG mixture models
Copyright (C) 2018 Oleksandr Frei
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License... |
f303bd6fb1d541924d9f501ffc5266b49f6bda48dfbf593b5ad0d139abd72ae1 | C++ | 72,533 | 1,269 | #include "IncludeDefine.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "SequenceFuns.h"
#include "OutSJ.h"
#include "sysRemoveDir.h"
#include "stringSubstituteAll.h"
#include SAMTOOLS_BGZF_H
#include "GlobalVariables.h"
#include "signalFromBAM.h"
#include "bamRemoveDuplicates.h"
#include "streamFuns.h"
... |
d114d8b8c36876c65314c50282b21fe7abb58fa6fcade7d05839b6ddf4693b26 | C++ | 73,322 | 2,008 | //
// PlexMethods.cpp
//
// Copyright (c) 1998-2013 Plexon, Inc, Dallas, Texas 75206
// www.plexon.com, support@plexon.com
//
// This code is provided as-is, in order to assist Plexon users who wish to
// use non-Windows platforms such as Linux. Plexon cannot provide support
// specific to any non-Windows... |
e406eccf75b6b58746a95d1c7ea7bc8e80ff974e438ef7c83074a46d4e62db9a | C++ | 77,378 | 2,427 | // 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 ... |
506c86020cb4efae2859dd1b4e3480c4091e4f9bac11f62b2039dfa17e1b5df5 | C++ | 88,663 | 1,749 | /*
bgmg - tool to calculate log likelihood of BGMG and UGMG mixture models
Copyright (C) 2018 Oleksandr Frei
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License... |
32d9d87d6fda81c92024fef1c224a117c69bd72558b21027f1a7850bfa110402 | C++ | 98,150 | 1,936 | //
// blocking.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 ... |
936a13ca4239e168b20888668c9cafd4a6d3a86a40ab2eed73fdf87935464197 | C++ | 99,741 | 3,082 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
dd637e23e2b79cad24da8e019fbd4df0218350453fe204b98bdd142f92c2fa4d | C++ | 102,224 | 2,000 | //
// mapping.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... |
d6f9643add42f8d7357cbf3afa214b8ebc5f142106b3999f91958eab3716f756 | C++ | 102,350 | 2,000 | //
// bulk_guarantee.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... |
4a4c2c037cd416a0a43263e193bc85d37d4a4b2ab81f104db44f27b95c478be7 | C++ | 115,931 | 3,643 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
242fe2171f7d75bcd47d1ce2f40812cc4ab1843d09aafe2232226d822efca4bb | C++ | 133,198 | 3,985 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
40fe607393a87b6ce98c7486972f5417b268f772c16a1bff829192e225e1335f | C++ | 158,028 | 4,904 | //
// write.cpp
// ~~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#if !defin... |
bfc481aaf7b1b9ea7ed1a85ff4e32faa0d633b17cc2117981505f9b318e6b074 | C++ | 174,525 | 4,997 | //
// read.cpp
// ~~~~~~~~
//
// Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com)
//
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
//
// Disable autolinking for unit tests.
#if !defined... |
c1b00be194f59a081edc1cef58bfce8db7f60e0bd731552bc164a672489e4586 | C++ | 178,430 | 4,858 | // 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 ... |
e1335a81e7a6820600ae0e3680e494d904f442026b111a21363ab81c4d8550bd | C++ | 180,228 | 5,664 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
1157f2c975560f7f9be23bfab499daa7f846e617d93a6bda9d2670c6a868a64b | C++ | 200,000 | 7,442 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
200c3513e3572ca4c2d931e2da6c4d76451955d198db79f53a4242ab81688307 | C++ | 200,000 | 5,756 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
22b0221aed14a4199f8ae03a24a298854fde66e7d14f53f718d60a203367fca5 | C++ | 200,000 | 6,344 | // 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 ... |
28c1fd37cebbd59c3461ca94c16157d75358bc205a0cced2936b64a14569337e | C++ | 200,000 | 8,280 | //
// 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 "urls_large... |
367e97a54ae39cd6f49d68c64fa131ab8fa3b8954a08bb7b34b5b86965f8d625 | C++ | 200,000 | 5,118 | #include "stdafx.h"
#include <math.h>
#include "dataanalysis.h"
#include "alglibinternal.h"
#include "linalg.h"
#include "statistics.h"
#include "alglibmisc.h"
#include "specialfunctions.h"
#include "solvers.h"
#include "optimization.h"
#include "diffequations.h"
#include "fasttransforms.h"
#include "integr... |
57585d66382993124d16ac86e4fa54acc8c1b151116db6c1fae3039df499eb51 | C++ | 200,000 | 5,075 | /* Generated by Cython 3.0.9 */
#ifndef PY_SSIZE_T_CLEAN
#define PY_SSIZE_T_CLEAN
#endif /* PY_SSIZE_T_CLEAN */
#if defined(CYTHON_LIMITED_API) && 0
#ifndef Py_LIMITED_API
#if CYTHON_LIMITED_API+0 > 0x03030000
#define Py_LIMITED_API CYTHON_LIMITED_API
#else
#define Py_LIMITED_API 0x03030000
#... |
944dc2379778a9404ed8dd7a3afb21c0c121e6081f049edffdcdf80cc4f88d0a | C++ | 200,000 | 6,055 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
a0b4f5ab3f30ad1ee4b1f032431922293dd98bd22f393089f0953c67a4d0dce2 | C++ | 200,000 | 4,954 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
a10e049d80388012d53266b7297cc82245e30159944b38cf69f31ab5069d3e91 | C++ | 200,000 | 7,389 | /**
* pugixml parser - version 1.11
* --------------------------------------------------------
* Copyright (C) 2006-2020, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
* Report bugs and download new versions at https://pugixml.org/
*
* This library is distributed under the MIT License. See notice at the end
... |
a44154e89d6feb17c559db986bc7fc41035b1ea574e7f8cba7a8919ad0d96da8 | C++ | 200,000 | 5,514 | //
// read_at.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... |
ecd6eb4144cf28112157e5648d15e45da0bb723c437fd0ab11a57c57e1a3e957 | C++ | 200,000 | 6,111 | //
// write_at.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 ... |
ff4bd60aa75154c7b29b34cae0dfce89fa2a9375c420f9af5e30a5e1870caafd | C++ | 200,000 | 6,646 | #include <stdio.h>
#include <time.h>
#include "ap.h"
// disable some irrelevant warnings
#if (AE_COMPILER==AE_MSVC)
#pragma warning(disable:4100)
#pragma warning(disable:4127)
#pragma warning(disable:4702)
#pragma warning(disable:4996)
#endif
#include "dataanalysis.h"
#include "alglibinternal.h"
#include "l... |
0e2875e1d7a3d5a5448b939d3f06e22fed372355ee8a20efeb3142619ffd5b52 | C++ | 200,004 | 7,170 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
1ee0766e7f700c04a79881dc7bbee357fc357474427137374295a5cd1f49de33 | C++ | 200,017 | 5,899 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
50c902835719084edfc9197de3403e5d98eda4f4da91cdd6fbb69c81e5331fd6 | C++ | 200,058 | 6,949 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
7a01baa1b0ce70efb76bc8b3fb911f18475040a89986ded329fd03d94017bb88 | C++ | 200,058 | 5,278 | /*************************************************************************
Copyright (c) Sergey Bochkanov (ALGLIB project).
>>> SOURCE LICENSE >>>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation (www.... |
75a11da44c802486bc6f65640aa48a730f0f684c5c07a42ba3cd1735eb3fb070 | C/C++ | 2 | 2 | |
0fc3e07fdf45e89b1b8654cb744dba8ed12311be1600986ce7bd7a448905aed3 | C/C++ | 49 | 4 |
#ifdef _MSC_VER
#pragma warning( pop )
#endif
|
84eb607a340a356e7bc8a88992b505277c103bd7e1746880800154a44e8682c3 | C/C++ | 57 | 3 | #define _USE_KNETFILE
#define BGZF_CACHE
#define BGZF_MT
|
abbe731b99b1de32bce2a8b899ee384f008c71883f3b144d4d36131b463cacae | C/C++ | 62 | 4 | #include "Parameters.h"
void genomeGenerate(Parameters &P);
|
447f2f74b6e3d744396a3b5a1917dcdce0fd3012cdab2c238648f7d0efb24864 | C/C++ | 78 | 4 | extern const char* errstr;
int planar_funcs_test();
int layout_funcs_test();
|
8c362ee417bed051cd49903d4bb49b6e2214c98e0d068bc610b3da929949bfc5 | C/C++ | 87 | 6 | #ifndef CODE_systemFunctions
#include <string>
std::string linuxProcMemory();
#endif
|
4cb602e3d61291f0611672f1e63ef16b0034439d49718cf5c59b2124870518f7 | C/C++ | 88 | 3 | //{{NO_DEPENDENCIES}}
// Microsoft Visual C++ generated include file.
// Used by app.rc
|
6da1efdc5aacdd913e0aba4fe990c092f5007eca8525bb52cc17c01a8a1e2b20 | C/C++ | 88 | 3 | #include <stdint.h>
void sortSuffixesBucket(char *G, void *ind, int indN, int indSkip); |
06412e22e5166c09c1c2f9639f84f7c930d8246864fe887b488890ec2f82527c | C/C++ | 105 | 4 | #ifndef OUTPUTSJ_DEF
#define OUTPUTSJ_DEF
void outputSJ(ReadAlignChunk** RAchunk, Parameters& P);
#endif
|
068797768ce12c98fa48bd59cd0636eafc2cf64dc84c590f2d3e708054e7c949 | C/C++ | 117 | 8 | #ifndef DEF_sysRemoveDir
#define DEF_sysRemoveDir
#include <string>
void sysRemoveDir(std::string dirName);
#endif |
ed20fbf78758766c499d7a62f8851d4b8ab311991c3086678e222834009d7a5b | C/C++ | 142 | 9 | /*
* main_testing.h
* peer
*
* Created by Oliver Stegle on 3/24/11.
* Copyright 2011 __MyCompanyName__. All rights reserved.
*
*/
|
1e6c025ec01771c966ee3773472a440e34e77dad07b5be9d542d05adea3a6af7 | C/C++ | 150 | 7 | #ifndef HDEF_binarySearch2
#define HDEF_binarySearch2
#include "IncludeDefine.h"
int binarySearch2(uint x, uint y, uint *X, uint *Y, int N);
#endif
|
15f402cde661a5cc115382d805f4c07e41640dfea1e54b8f692c97acae8e9ae9 | C/C++ | 157 | 9 | #ifndef GLOBAL_VARIABLES_DEF
#define GLOBAL_VARIABLES_DEF
#include "ThreadControl.h"
extern Stats g_statsAll;
extern ThreadControl g_threadChunks;
#endif
|
d730a66e4059292b7fc2d00b4666facb3eb28637a89fef8754ba6189f7f2ebc7 | C/C++ | 163 | 8 | #ifndef CODE_bam_cat
#define CODE_bam_cat
#include "htslib/htslib/sam.h"
int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
#endif
|
a4f10a9e7579a8111d87666d98abf86fb25fc8b1b9dcac6ef280a006e7639567 | C/C++ | 164 | 3 | /* Additional files bcp somehow misses when enumerating required boost files*/
#include <boost/parameter/aux_/overloads.hpp>
#include <boost/endian/conversion.hpp>
|
fe5b55ee97274b592147eb5dfb0d87a5cecbc02a8703655bad0447f06e9f7bcb | C/C++ | 166 | 2 | const char *model_to_matlab_structure(mxArray *plhs[], struct model *model_);
const char *matlab_matrix_to_model(struct model *model_, const mxArray *matlab_struct);
|
359b6936ed394acbb6b3439b3cc4bdc97c6ba58ce48f6c4c49541620bd0c8e19 | C/C++ | 168 | 10 | #ifndef BLOCKS_OVERLAP_DEF
#define BLOCKS_OVERLAP_DEF
#include "IncludeDefine.h"
#include "Transcript.h"
uint blocksOverlap(Transcript &t1, Transcript &t2);
#endif
|
fe4af9be5d3872145195d45b33ea44234b36123c34b723eef5094558fdbdad81 | C/C++ | 168 | 9 | #ifndef TIME_FUNCTIONS_DEF
#define TIME_FUNCTIONS_DEF
#include <string>
#include <time.h>
string timeMonthDayTime();
string timeMonthDayTime(time_t &rawTime);
#endif
|
c3713f7dfff0f2e66c38170cdae17cdc8bad257f55b507f9d113dc1e22ba8148 | C/C++ | 170 | 9 | #ifndef H_AlignVsTranscript
#define H_AlignVsTranscript
namespace AlignVsTranscript
{
enum {Intron=0, ExonIntron=1, ExonIntronSpan=2, Concordant=3, N=4};
};
#endif |
13fc9fee26fa88b86648a7f68c2d50852d1815924dc5b7a50f1930568f9b9e16 | C/C++ | 178 | 8 | #ifndef DEF_stringReplaceAll
#define DEF_stringReplaceAll
#include <string>
void stringSubstituteAll(std::string& str, const std::string& from, const std::string& to);
#endif
|
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