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//---------------------------------------------------------------------------// // 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...
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#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...
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#include "ReadAlign.h" #include "SequenceFuns.h" #include "ErrorWarning.h" uint64 ReadAlign::outputSpliceGraphSAM(Transcript const &trOut, uint nTrOut, uint iTrOut, ostream *outStream) { uint64 outStreamPos0=(uint64)outStream->tellp(); uint16 samFLAG=0; if (readFilter=='Y') samFLAG |= 0x200; //...
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//heap.cpp ////////////////////////////////////////////////////////////////////////////// // The heap index (return by the push() method) is a map from the grid // // address to the index of heap's internal data representation. // // ...
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// // daemon.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/io_context.hpp> #include <...
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/** ReadAlign - one read, all alignments */ #include "IncludeDefine.h" #include "Parameters.h" #include "Transcript.h" #include "ReadAlign.h" #include "ErrorWarning.h" void ReadAlign::storeAligns (uint iDir, uint Shift, uint Nrep, uint L, uint indStartEnd[2], uint iFrag) {//fill in alignment data #ifdef OFF_BE...
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// 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...
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// g++ -DNDEBUG -O3 -I.. benchEigenSolver.cpp -o benchEigenSolver && ./benchEigenSolver // options: // -DBENCH_GMM // -DBENCH_GSL -lgsl /usr/lib/libcblas.so.3 // -DEIGEN_DONT_VECTORIZE // -msse2 // -DREPEAT=100 // -DTRIES=10 // -DSCALAR=double #include <Eigen/Array> #include <Eigen/QR> #include <bench/BenchUt...
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// // blocking_token_tcp_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 ...
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#include <boost/config.hpp> #ifndef BOOST_MSVC int main() { } #else #if defined(BOOST_MSVC) #pragma warning(disable: 4786) // identifier truncated in debug info #pragma warning(disable: 4710) // function not inlined #pragma warning(disable: 4711) // function selected for automatic inline expansion #pragma warnin...
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// Boost string_algo library trim_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 htt...
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// g++ -DNDEBUG -O3 -I.. benchEigenSolver.cpp -o benchEigenSolver && ./benchEigenSolver // options: // -DBENCH_GMM // -DBENCH_GSL -lgsl /usr/lib/libcblas.so.3 // -DEIGEN_DONT_VECTORIZE // -msse2 // -DREPEAT=100 // -DTRIES=10 // -DSCALAR=double #include <iostream> #include <Eigen/Core> #include <Eigen/QR> #in...
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#include "SoloFeature.h" #include "serviceFuns.cpp" #include <math.h> void SoloFeature::cellFiltering() { if (pSolo.cellFilter.type[0]=="None" || nCB<1) {//no filtering, or no cells to filter return; }; switch(featureType) { default: return; //filtering not done for o...
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// // daemon.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/io_context.hpp> #include <...
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// // posix_chat_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 <cstdlib> #inclu...
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// // 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 // //------------------...
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// 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 fi...
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// // async_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 <iostream> #include <istre...
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// // 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...
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// (C) Copyright Marshall Clow 2018 // 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 <iterator> // for std::distance #include <cassert> // for assert #include <boost...
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// // bind_allocator.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...
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// 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...
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//===----------------------------------------------------------------------===// // // 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. // //===----------------------------------------...
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// (C) Copyright Eric Niebler 2005. // Use, modification and distribution are subject to the // Boost Software License, Version 1.0. (See accompanying file // LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) #include <iostream> #include <vector> #include <boost/utility/enable_if.hpp> #include <boos...
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// // 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 // //------------------...
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// (C) Copyright Eric Niebler 2005. // Use, modification and distribution are subject to the // Boost Software License, Version 1.0. (See accompanying file // LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) #include <iostream> #include <valarray> #include <boost/utility/enable_if.hpp> #include <bo...
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// // Copyright (c) 2013-2017 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 ...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. Eigen itself is part of the KDE project. // // Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public //...
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//---------------------------------------------------------------------------// // 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...
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/* Copyright (c) 2002-2005 CrystalClear Software, Inc. * Use, modification and distribution is subject to the * Boost Software License, Version 1.0. (See accompanying * file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) * Author: Jeff Garland, Bart Garst * $Date$ */ #ifndef BOOST_DATE_TIME_SOURCE #...
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/* * 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 Andrey Semashev */ /*! * \file lockpool.cpp * * This file contains implementation of the ...
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// Boost.Assign library // // Copyright Thorsten Ottosen 2003-2004. Use, modification and // distribution is subject to the Boost Software License, Version // 1.0. (See accompanying file LICENSE_1_0.txt or copy at // http://www.boost.org/LICENSE_1_0.txt) // // For more information, see http://www.boost.org/libs/ass...
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// 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 ...
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// // stream_descriptor.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 fo...
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/** * Copyright 2017-present, Facebook, Inc. * All rights reserved. * * This source code is licensed under the license found in the * LICENSE file in the root directory of this source tree. */ #include <pybind11/detail/common.h> #include <pybind11/pybind11.h> #include <torch/torch.h> // @manual=//caffe2:torch_ex...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2011 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...
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//---------------------------------------------------------------------------// // 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...
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#include "SoloFeature.h" #include "streamFuns.h" #include "ErrorWarning.h" #include "SoloFeatureTypes.h" #include "serviceFuns.cpp" void SoloFeature::loadRawMatrix() { //make directories if (P.runModeIn.size()<3) { string errOut = "Exiting because of fatal PARAMETER error: --runMode soloCellFilteri...
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// BSD 3-Clause License // // Copyright (c) 2019, Karan Aggarwal (karan@iisc.ac.in) // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // 1. Redistributions of source code must retain the a...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2009-2010 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...
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/* Copyright (c) Marshall Clow 2011-2012. Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) For more information, see http://www.boost.org Test non-string cases; vector and list */ #include <boost/config.h...
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// BSD 3-Clause License // // Copyright (c) 2019, Karan Aggarwal (karan@iisc.ac.in) // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // 1. Redistributions of source code must retain the a...
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#include <iostream> #include <Eigen/Geometry> #include <bench/BenchTimer.h> using namespace Eigen; using namespace std; template<typename Q> EIGEN_DONT_INLINE Q nlerp(const Q& a, const Q& b, typename Q::Scalar t) { return Q((a.coeffs() * (1.0-t) + b.coeffs() * t).normalized()); } template<typename Q> EIGEN_DONT_...
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// // 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 ...
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// // request_parser.cpp // ~~~~~~~~~~~~~~~~~~ // // Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com) // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // #include "request_parser.hpp" #...
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// Boost string_algo library iterator_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...
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#include "emitterstate.h" #include "exceptions.h" namespace YAML { EmitterState::EmitterState(): m_isGood(true), m_curIndent(0), m_requiresSeparation(false) { // start up m_stateStack.push(ES_WAITING_FOR_DOC); // set default global manipulators m_charset.set(EmitNonAscii); m_strFmt.set(Auto); m_boolFm...
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// (C) Copyright Jonathan Turkanis 2003. // 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/libs/iostreams for documentation. // To configure Boost to work with zlib, see the // installa...
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// // 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 <boost/asio.hpp> #include <boost/bind/...
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// 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...
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//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 // -I /home/gael/Coding/LinearAlgebra/CSparse/...
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//g++-4.4 -DNOMTL -Wl,-rpath /usr/local/lib/oski -L /usr/local/lib/oski/ -l oski -l oski_util -l oski_util_Tid -DOSKI -I ~/Coding/LinearAlgebra/mtl4/ spmv.cpp -I .. -O2 -DNDEBUG -lrt -lm -l oski_mat_CSC_Tid -loskilt && ./a.out r200000 c200000 n100 t1 p1 #define SCALAR double #include <iostream> #include <algor...
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//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 // -I /home/gael/Coding/LinearAlgebra/CSparse/...
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// // third_party_lib.cpp // ~~~~~~~~~~~~~~~~~~~ // // Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com) // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // #include <boost/asio.hpp> #in...
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#include "ReadAlignChunk.h" #include <pthread.h> #include "ErrorWarning.h" ReadAlignChunk::ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, int iChunk) : P(Pin), mapGen(genomeIn) {//initialize chunk iThread=iChunk; if ( P.quant.yes ) {//allocate transcriptome structures chunkTr=...
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// // Copyright (c) 2016-2017 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...
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// 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...
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/** * 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 "meter.h" #include "utils.h" #include <algorithm> #include <cmath> #include <iomanip> #include <limits...
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// // chat_server.cpp // ~~~~~~~~~~~~~~~ // // Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com) // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // #include <algorithm> #include <cstdli...
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#include "Variation.h" #include "streamFuns.h" #include "SequenceFuns.h" #include "TimeFunctions.h" #include "serviceFuns.cpp" #include "ErrorWarning.h" Variation::Variation (Parameters &Pin, vector <uint> &chrStartIn, map <string,uint> &chrNameIndexIn, bool yesVar) : P(Pin), chrStart(chrStartIn), chrNameIndex(chrName...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. Eigen itself is part of the KDE project. // // Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public //...
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// 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 ...
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// // blocking_tcp_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/...
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// 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...
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#include "sjdbInsertJunctions.h" #include "sjdbLoadFromStream.h" #include "sjdbLoadFromFiles.h" #include "sjdbPrepare.h" #include "ErrorWarning.h" #include "GTF.h" #include "sjdbBuildIndex.h" #include "streamFuns.h" #include "genomeParametersWrite.h" void sjdbInsertJunctions(Parameters & P, Genome & mapGen, Genome & m...
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#include "SoloFeature.h" #include "streamFuns.h" #include "TimeFunctions.h" #include "SequenceFuns.h" #include "serviceFuns.cpp" #include "soloInputFeatureUMI.h" void SoloFeature::countSmartSeq() { time_t rawTime; //nCB=pSolo.cbWLsize; //all cells are recorded //nCB, indCB are recorded in sumThre...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2011 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...
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// #define EIGEN_TAUCS_SUPPORT // #define EIGEN_CHOLMOD_SUPPORT #include <Eigen/Sparse> // g++ -DSIZE=10000 -DDENSITY=0.001 sparse_cholesky.cpp -I.. -DDENSEMATRI -O3 -g0 -DNDEBUG -DNBTRIES=1 -I /home/gael/Coding/LinearAlgebra/taucs_full/src/ -I/home/gael/Coding/LinearAlgebra/taucs_full/build/linux/ -L/home/gael/Co...
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// 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...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2010 Gael Guennebaud <g.gael@free.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software ...
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/** * 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 "productquantizer.h" #include <algorithm> #include <iostream> #include <numeric> #include <stdexcept> ...
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// // request_parser.cpp // ~~~~~~~~~~~~~~~~~~ // // Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com) // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // #include "request_parser.hpp" #...
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// // request_parser.cpp // ~~~~~~~~~~~~~~~~~~ // // Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com) // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // #include "request_parser.hpp" #...
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// // request_parser.cpp // ~~~~~~~~~~~~~~~~~~ // // Copyright (c) 2003-2022 Christopher M. Kohlhoff (chris at kohlhoff dot com) // // Distributed under the Boost Software License, Version 1.0. (See accompanying // file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) // #include "request_parser.hpp" #...
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// 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...
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// // blocking_tcp_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/...
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// #define EIGEN_TAUCS_SUPPORT // #define EIGEN_CHOLMOD_SUPPORT #include <iostream> #include <Eigen/Sparse> // g++ -DSIZE=10000 -DDENSITY=0.001 sparse_cholesky.cpp -I.. -DDENSEMATRI -O3 -g0 -DNDEBUG -DNBTRIES=1 -I /home/gael/Coding/LinearAlgebra/taucs_full/src/ -I/home/gael/Coding/LinearAlgebra/taucs_full/build/lin...
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//---------------------------------------------------------------------------// // 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...
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//---------------------------------------------------------------------------// // 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...
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// g++ -O3 -DNDEBUG -I.. -L /usr/lib64/atlas/ benchBlasGemm.cpp -o benchBlasGemm -lrt -lcblas // possible options: // -DEIGEN_DONT_VECTORIZE // -msse2 // #define EIGEN_DEFAULT_TO_ROW_MAJOR #define _FLOAT #include <iostream> #include <Eigen/Core> #include "BenchTimer.h" // include the BLAS headers extern "C" {...
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#include "adaptertrimmer.h" #include "matcher.h" #include "simd.h" AdapterTrimmer::AdapterTrimmer(){ } AdapterTrimmer::~AdapterTrimmer(){ } bool AdapterTrimmer::trimByOverlapAnalysis(Read* r1, Read* r2, FilterResult* fr, int diffLimit, int overlapRequire, double diffPercentLimit) { OverlapResult ov = OverlapAna...
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// 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...
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#include "resolve_attempt_udp.h" #include "api_config.h" #include "resolver_impl.h" #include "socket_utils.h" #include <boost/asio/ip/multicast.hpp> #include <loguru.hpp> #include <sstream> using namespace lsl; namespace asio = lslboost::asio; using err_t = const lslboost::system::error_code &; resolve_attempt_udp::r...
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/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8 // xml_wgrammar.cpp: // (C) Copyright 2002 Robert Ramey - http://www.rrsd.com . // Use, modification and distribution is subject to the Boost Software // License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at // http://w...
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// Boost string_algo library example 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 htt...
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#include "Transcript.h" bool Transcript::convertGenomeCigar(Genome &genOut, Transcript & A) { auto &coBl=genOut.genomeOut.convBlocks; auto cBit=coBl.begin(); cBit = std::upper_bound(cBit, coBl.end(), array<uint64,3> {gStart,0,0}, [](const array<uint64,3> &t1, const array<u...
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#include "SoloBarcode.h" #include "serviceFuns.cpp" #include "SoloCommon.h" #include "SequenceFuns.h" #include "ParametersSolo.h" void wlAddMismatches(uint32 nMM, uint32 cbLen, vector<uintCB> &wl, vector<uintCB> &wlEd1, vector<uint32> &wlInd1); void SoloBarcode::sortWhiteList(ParametersSolo *pSolo) { totalSize=0;...
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// // blocking_token_tcp_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 ...
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/* Copyright (c) Marshall Clow 2011-2012. Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) For more information, see http://www.boost.org */ #include <boost/config.hpp> #include <boost/algorithm/hex.hpp> #...
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// // 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 // //------------------...
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// 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...
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#include <string> #include <sstream> #include <iostream> #include <fstream> #include <iomanip> #include <map> #include <list> using namespace std; // this function takes a line that may contain a name and/or email address, // and returns just the name, while fixing the "bad cases". std::string contributor_name(const ...
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//#include "blocksOverlap.h" #include "ChimericDetection.h" #include "ChimericSegment.h" #include "ReadAlign.h" int chimericAlignScore (ChimericSegment & seg1, ChimericSegment & seg2) { int chimScore=0; uint chimOverlap = seg2.roS>seg1.roS ? (seg2.roS>seg1.roE ? 0 : seg1.roE-seg2.roS+1) : (seg2.roE<seg1.roS ?...
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//---------------------------------------------------------------------------// // 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...
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#include "jsonreporter.h" JsonReporter::JsonReporter(Options* opt){ mOptions = opt; mDupHist = NULL; mDupRate = 0; } JsonReporter::~JsonReporter(){ } void JsonReporter::setDup(double dupRate) { mDupRate = dupRate; } void JsonReporter::setInsertHist(atomic_long* insertHist, int insertSizePeak) { ...
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#include <cstdint> #include <memory> #include "draco/compression/decode.h" #include "draco/mesh/mesh_stripifier.h" namespace { struct FreeDeleter { void operator()(void *p) const { ::free(p); } }; /// Lookup table that maps numbers 0 to 255 to the index of the first non-zero /// bit, or 0 if all bits are 0. conste...
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// // generic/seq_packet_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) // // Di...
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//---------------------------------------------------------------------------// // 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...
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// // set_error.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...
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// SharedMemory.cpp // Gery Vessere - gvessere@illumina.com, gery@vessere.com // An abstraction over both SysV and POSIX shared memory APIs #include "SharedMemory.h" #include <sstream> #include <sys/mman.h> #include <sys/shm.h> #include <sys/stat.h> /* For mode constants */ #include <fcntl.h> /* For O...