sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1c459dc0735836aa98e434261f5d0bb7dca932b2ca780b7428d578c21d4f609b | C++ | 15,311 | 357 | /*
* Copyright (C) 2019-2026 Matthias Klumpp <matthias@tenstral.net>
*
* Licensed under the GNU Lesser General Public License Version 3
*
* This program 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 Founda... |
6c98fb3a2205ada17a573798b4e3c8dcf4a30f5cc93251eb44c1c78e7dec0ca4 | C++ | 15,322 | 316 | #include "Parameters.h"
#include "Util.h"
#include "DBWriter.h"
#include "CommandCaller.h"
#include "Debug.h"
#include "FileUtil.h"
#include "cascaded_clustering.sh.h"
#include "nucleotide_clustering.sh.h"
#include "clustering.sh.h"
#include <cassert>
void setWorkflowDefaults(Parameters *p) {
p->spacedKmer = tru... |
a4ca0fc687ae8253f144fe33d03bc82f55f1fc6060deae5d06579cba334a10c9 | C++ | 15,436 | 536 | /*
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under both the BSD-style license (found in the
* LICENSE file in the root directory of this source tree) and the GPLv2 (found
* in the COPYING file in the root directory of this source tree).
*/
#include "Opti... |
4c6f3938492ec33d62840f7fcf6e5037451ec6087d4e41866e5db55dc2a12500 | C++ | 15,528 | 490 | #include "FileUtil.h"
#include "Util.h"
#include "Debug.h"
#include "simd.h"
#include <cstddef>
#include <cstring>
#include <climits>
#include <algorithm>
#include <stdio.h>
#include <fcntl.h>
#include <unistd.h>
#include <sys/stat.h>
#include <sys/statvfs.h>
#include <sys/types.h>
#include <sys/mman.h>
#include <sys... |
498d96e494f7748f92d77eb39b02bd55b0e7fa0dc94ed01d8fbf5a934c15053f | C++ | 15,687 | 338 | #include "MsaFilter.h"
#include "Parameters.h"
#include "PSSMCalculator.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "tantan.h"
#include "IndexReader.h"
#include "Masker.h"
#ifdef OPENMP
#include <omp.h>
#endif
int result2profile(int argc, const ch... |
2c3a03ae63ab15d06289673f5de0a51be6867e923bd2d08c2f22128da0e2cf6a | C++ | 15,755 | 391 | #include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/inner_product_layer.hpp"
#include "caffe/test/test_caffe_main.hpp"
#include "caffe/test/test_gradient_check_util.hpp"
namespace caffe {
#ifndef CPU_ONLY
extern cudaDev... |
e9a9aa6d5ff396b15d14bcf663ac611fb912b5feb55d7703fb232ac31092e78e | C++ | 15,788 | 415 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
c6d71d817fa81a1292036befb383523bd29fa43e09fd7c1dcbff56cb409386c9 | C++ | 15,883 | 375 | /**
* Copyright 2014-2025, XGBoost Contributors
* \file simple_dmatrix.cc
* \brief the input data structure for gradient boosting
* \author Tianqi Chen
*/
#include "simple_dmatrix.h"
#include <algorithm>
#include <limits>
#include <numeric> // for accumulate
#include <type_traits>
#include <vector>
#include "..... |
74fff23b152aefcb15b607119fc5a333322c436b58cb5879ad5751640d2fea05 | C++ | 16,089 | 469 | #ifdef USE_OPENCV
#include <string>
#include <vector>
#include "boost/scoped_ptr.hpp"
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/data_layer.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caffe/util/db.hpp"
#include "caffe/util/io... |
f2bf03b48236385d3fcc28f157195b881754ad73d17696f09a8f367bf3beac09 | C++ | 16,102 | 487 | #include "stdafx.h"
#include "Compat.h"
#include "AffineGap.h"
#include "LandauVishkin.h"
#include "mapq.h"
#include "Read.h"
#include "BaseAligner.h"
#include "Bam.h"
#include "exit.h"
#include "Error.h"
// #define PRINT_SCORES 1
AffineGapWithCigar::AffineGapWithCigar(
int i_matchReward,
int i_subPenalty,
... |
aa3e40a24677d23e76503717df96f7b0105c0b4e4faeebcea27dcc54a5c7792d | C++ | 16,103 | 397 | #include <algorithm>
#include <vector>
#include "caffe/filler.hpp"
#include "caffe/layers/base_conv_layer.hpp"
#include "caffe/util/im2col.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void BaseConvolutionLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
c... |
431c61cf0ebf829b7447406ff8145d7470b4c9e429b9ee691f2024e337dd3d27 | C++ | 16,133 | 514 | /**
* Copyright 2018-2025, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include "../../../src/common/bitfield.h"
#include "../../../src/common/categorical.h"
#include "../../../src/tree/io_utils.h" // for DftBadValue
#include "../filesystem.h"
#include "../helpers.h"
#include "xgboost/tree_model.h"
namespace ... |
6c5840dd8f248f2b9314ce289341e8cff9cb5477142b9e18f2c16fdb669a066e | C++ | 16,134 | 503 | /*!
* Copyright 2014-2020 by Contributors
* \file cli_main.cc
* \brief The command line interface program of xgboost.
* This file is not included in dynamic library.
*/
#include <dmlc/timer.h>
#include <xgboost/base.h>
#include <xgboost/data.h>
#include <xgboost/json.h>
#include <xgboost/learner.h>
#include <xgbo... |
b0996a763317cc1007114ce438f7a18e66a2da18b98c4c2ebea7bf6fbf0fb27b | C++ | 16,219 | 343 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "Alignment.h"
#include "itoa.h"
#include "BacktraceTranslator.h"
#include "AlignmentSymmetry.h"
#include "DistanceCalculato... |
005e51339269b7e9eaa3b0986fc6dc43a0ca71fffe62c2c4b96d362b1ff6e689 | C++ | 16,349 | 232 | /* $Id: $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act... |
143b297ac38ec2d2e380e64e4f60c69f99d996f2b2fbd194d9744c5753b36a3d | C++ | 16,478 | 530 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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, or
* (at your opt... |
44c4ae91ddc13cd747c9989df01086b399ff23d69e4242d49f2922ee4cfa3a64 | C++ | 16,497 | 382 | /*!
* Copyright 2017-2023 by Contributors
* \file hist_util.cc
*/
#include <vector>
#include <limits>
#include <algorithm>
#include "../data/gradient_index.h"
#include "hist_util.h"
#include <sycl/sycl.hpp>
namespace xgboost {
namespace sycl {
namespace common {
/*!
* \brief Fill histogram with zeroes
*/
templ... |
f96094100cbb00d090854bf576f024e6fda2244369f9c075b6ab5c601b57f906 | C++ | 16,502 | 555 | #include <vector>
#include "gtest/gtest.h"
#include "caffe/filler.hpp"
#include "caffe/test/test_caffe_main.hpp"
namespace caffe {
template <typename Dtype>
class ConstantFillerTest : public ::testing::Test {
protected:
ConstantFillerTest()
: blob_(new Blob<Dtype>()),
filler_param_() {
filler_... |
272ffa358d81ff1d8f18c37666101eb117f8f1c8b515f2896dd79218cb5a2265 | C++ | 16,514 | 442 | /**
* Copyright 2016-2025, XGBoost Contributors
*/
#include <xgboost/data.h>
#include <array> // std::array
#include <limits> // std::numeric_limits
#include <memory> // std::unique_ptr
#include "../../../src/data/adapter.h" // ArrayAdapter
#include "../../../src/data/simple_dmatrix.h" // SimpleDMatrix... |
907ab64fa70d078a4886f9f48a7021b18dd6f2c27e8e0e9c2064fad8f2f73fa4 | C++ | 16,631 | 424 | /**
* Copyright 2016-2024, XGBoost contributors
*/
#include "test_metainfo.h"
#include <dmlc/io.h>
#include <gmock/gmock.h>
#include <xgboost/data.h>
#include <memory>
#include <string>
#include "../collective/test_worker.h" // for TestDistributedGlobal
#include "../filesystem.h" // dmlc::TemporaryDi... |
ed8fb6dd97a6c59d2c06d0aade752309da345496e9bafda8e71852b18ec80c91 | C++ | 16,789 | 520 | /*
* Copyright 2026, Ben Langmead <ben.langmead@gmail.com> and
* Rone Charles <rone_charles@fastmail.com>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
/*
* Block reader that keeps parsing out of the input critical section.
* See fast_reader.h.
*/
#include "fast_reader.h"
... |
78fca6405086073ace859315b31822c3e016e99a9f41acbfac19b2060594615d | C++ | 16,836 | 415 | /**
* Copyright 2017-2023 by XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h>
#include <xgboost/json.h>
#include <xgboost/objective.h>
#include <numeric> // for iota
#include "../../../src/common/linalg_op.h" // for begin, end
#include "../../../src/objective/adaptive.h"
#include "../... |
a1e72515aeb089346b72cc81fa2b84eff233b6be26d9d1dbb3681f4a8709c0a1 | C++ | 16,937 | 433 | /*++
Module Name:
PairedReadMatcher.cpp
Abstract:
Match paired-end reads coming in from different streams
Authors:
Bill Bolosky, November, 2012
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include <map>
#include "Compat.h"
#include "Util.h"
#include "Read.h"
#i... |
faf9bf75a9ab729c874e81cd10648bef932564339e40d1bc83da23cd522e171a | C++ | 16,990 | 600 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
a79af78556802b3de58f30eda4dbb67bf824b57656847e4de06510fe96ea8848 | C++ | 17,032 | 444 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
66b030b97b1bfa8a71fbba0698895dec545aacc502834619577bd171f23f64dd | C++ | 17,046 | 553 | // Author: Martin C. Frith 2010
// SPDX-License-Identifier: MPL-2.0
#include "tantan.h"
#include "mcf_simd.h"
#include <algorithm> // fill, max
#include <cassert>
#include <cmath> // pow, abs
#include <iostream> // cerr
#include <numeric> // accumulate
#include <vector>
#define BEG(v) ((v).empty() ? 0 : &(v).fro... |
661e0f7edcd15e287188cf1e76e928cabccc621c26b886b337706a192b1e992f | C++ | 17,055 | 455 | #include "SubstitutionMatrix.h"
#include "Util.h"
#include "Debug.h"
#include "LambdaCalculation.h"
#include <cstring>
#include <cctype>
#include <algorithm>
#include <fstream>
#include <cmath>
#include <climits>
SubstitutionMatrix::SubstitutionMatrix(const char *filename, float bitFactor, float scoreBias) : bitFacto... |
c1aad8da2fb6dcd03127d9f2846b5fce408b54d7988cf38d1516bfbbd573dc3a | C++ | 17,227 | 484 | /**
* Copyright 2021-2024, XGBoost Contributors
*/
#include "auc.h"
#include <algorithm>
#include <array>
#include <atomic>
#include <functional>
#include <limits>
#include <memory>
#include <numeric>
#include <tuple>
#include <utility>
#include <vector>
#include "../common/algorithm.h" // ArgSort
#include "... |
928ceb638ac0feec90054e5c5b18bee324c14e976061c9262862c0161c04c034 | C++ | 17,247 | 332 | #include "LinsearchIndexReader.h"
#include "FileUtil.h"
#include "PrefilteringIndexReader.h"
#include "Debug.h"
#include "Timer.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "KmerIndex.h"
#include "kmersearch.h"
#ifndef SIZE_T_MAX
#define SIZE_T_MAX ((size_t) -1)
... |
eaecd0380533ccaabcfd69101c129387ddebf8dd70f46ecc40ed1573c8f90b62 | C++ | 17,411 | 431 | /*++
Module Name:
ComputeROC.cpp
Abstract:
Take a SAM file with simulated reads and compute a ROC curve from it.
Authors:
Bill Bolosky, December, 2012
Environment:
`
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "SAM.h"
#include "Bam.h"
#include "Genome.h"
#include... |
aed6e251cbb4ea6681f35713b7c2c06a0b575f3a0b73e38607f82e2d834c42df | C++ | 17,436 | 729 | /*
ahklib.cpp
Original code by Steve Gray.
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
Permission is granted to anyone to use this software for any purpose,
including commercial applicat... |
152752f65c0f9e295582a9343533aa3995dbfb69b5976e1b8b771bc71eac0d26 | C++ | 17,505 | 415 | #include <iomanip>
#include <itoa.h>
#include "Matcher.h"
#include "Util.h"
#include "Parameters.h"
#include "StripedSmithWaterman.h"
#include <fast_float/fast_float.h>
#include "CovSeqidQscPercMinDiag.lib.h"
#include "CovSeqidQscPercMinDiagTargetCov.lib.h"
Matcher::Matcher(int querySeqType, int maxSeqLen, BaseMatri... |
59ae8d68be14c865c3ccd14731a903a7b8df84c6aaf2c21f4bb11cb85a98f034 | C++ | 17,544 | 476 | #ifdef USE_OPENCV
#include <opencv2/highgui/highgui_c.h>
#include <stdint.h>
#include <algorithm>
#include <map>
#include <string>
#include <utility>
#include <vector>
#include "opencv2/core/core.hpp"
#include "opencv2/highgui/highgui.hpp"
#include "opencv2/imgproc/imgproc.hpp"
#include "caffe/data_transformer.hpp"
... |
9fdc66dfb4a90350b5e8c7d2e6a074c4731adef0d4fcdf39c423f0a5232c366b | C++ | 17,768 | 369 | // dear imgui: Platform Binding for GLFW
// This needs to be used along with a Renderer (e.g. OpenGL3, Vulkan..)
// (Info: GLFW is a cross-platform general purpose library for handling windows, inputs, OpenGL/Vulkan graphics context creation, etc.)
// (Requires: GLFW 3.1+)
// Implemented features:
// [X] Platform: Cl... |
ab6b5ad7408e73f0fdc5ac6270af12f357a37146104c22a1e5d5122532a9b351 | C++ | 17,796 | 655 | #include "stdafx.h"
#include "script.h"
#include "globaldata.h"
Object *ScriptModule::sPrototype;
ResultType ScriptModule::Invoke(IObject_Invoke_PARAMS_DECL)
{
Var *var = aName ? FindImportableVar(aName) : nullptr;
if (!var)
return ObjectBase::Invoke(IObject_Invoke_PARAMS);
if (IS_INVOKE_SET && aParamCount ==... |
375eedb87bddd7870a13d7526d02b6c38a17cae24695b935e158682ee4099735 | C++ | 17,964 | 490 | /**
* Copyright 2020-2023 by XGBoost contributors
*/
#include "rank_metric.h"
#include <dmlc/omp.h>
#include <dmlc/registry.h>
#include <algorithm> // for stable_sort, copy, fill_n, min, max
#include <array> // for array
#include <cmath> ... |
e1c1025a2d1200305ed51904358633462c1e5558d805e676a7b687f8aacd13ee | C++ | 17,994 | 496 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <cmath>
#include <ksw2.h>
//#include "gaba_wrap.h" /* multiple target configuration: gcc example.c libgaba.a */
#include <stdint.h>
#include <stdio.h>
#includ... |
84679b2881da822083bac02fcbc67ea72f25aa985cff7e672b73a50e544728f0 | C++ | 18,018 | 461 | /* Based on orf.cpp from NCBI C++ Toolkit
* License:
* $Id: orf.cpp 65735 2014-12-23 18:23:27Z astashya $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This soft... |
38ea04c1850bfa9eff8403203dcc5b4767c65ecbc7cd013b8f1de30b7074d991 | C++ | 18,034 | 370 | // dear imgui: Platform Binding for SDL2
// This needs to be used along with a Renderer (e.g. DirectX11, OpenGL3, Vulkan..)
// (Info: SDL2 is a cross-platform general purpose library for handling windows, inputs, graphics context creation, etc.)
// (Requires: SDL 2.0. Prefer SDL 2.0.4+ for full feature support.)
// Im... |
68c4feca4c0077858aa8f0484e7b8bb898ed46f0703c7fc04530212be54884ca | C++ | 18,042 | 545 | #ifdef USE_OPENCV
#include <opencv2/core/core.hpp>
#endif // USE_OPENCV
#include <string>
#include <vector>
#include "caffe/data_transformer.hpp"
#include "caffe/util/io.hpp"
#include "caffe/util/math_functions.hpp"
#include "caffe/util/rng.hpp"
namespace caffe {
template<typename Dtype>
DataTransformer<Dtype>::Da... |
ec7c92f0d353dee7d68778bf91fd68b05adb538b32882b0a5f02b5db0f7f6423 | C++ | 18,172 | 506 | #include <cstdio>
#include <string>
#include <vector>
#include "boost/algorithm/string.hpp"
#include "caffe/solver.hpp"
#include "caffe/util/format.hpp"
#include "caffe/util/hdf5.hpp"
#include "caffe/util/io.hpp"
#include "caffe/util/upgrade_proto.hpp"
namespace caffe {
template<typename Dtype>
void Solver<Dtype>::... |
1fcaaafd59bb0ae1c430fece253f982a24a1c9c99f486c2a84c030970c98c626 | C++ | 18,315 | 429 | // dear imgui: Renderer + Platform Binding for Allegro 5
// (Info: Allegro 5 is a cross-platform general purpose library for handling windows, inputs, graphics, etc.)
// Implemented features:
// [X] Renderer: User texture binding. Use 'ALLEGRO_BITMAP*' as ImTextureID. Read the FAQ about ImTextureID!
// [X] Platform:... |
f8868644f8b104a9aebf9c3cfabfd5cb46d233e48e4ca7acc2ba8ce0781b269f | C++ | 18,319 | 342 | //
// Implemented by Martin Steinegger, Lars vdd
//
#include "AlignmentSymmetry.h"
#include <climits>
#include <new>
#include <algorithm>
#include "Parameters.h"
#include "Util.h"
#include "Debug.h"
#include "FastSort.h"
#include <cmath>
#ifdef OPENMP
#include <omp.h>
#endif
#define LEN(x, y) (x[y+1] - x[y])
void Al... |
d8505b7bfbf94ff9b0f01a6a19030ccfe5f89208e293b215a8a819d1054e77c3 | C++ | 18,415 | 557 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
383e5c91b7c5ee1824260ef47161e9af0ed779d25549b2dc1ca1dfe20e259ff4 | C++ | 18,510 | 498 | // 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 ... |
a962dfac27d7a0d7e494cd1412bf29be401945fabc57b5f1c294eea29fb9d8c5 | C++ | 18,546 | 458 | #include "Matcher.h"
#include "MsaFilter.h"
#include "Parameters.h"
#include "PSSMCalculator.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "CompressedA3M.h"
#include "MathUtil.h"
#include "simd.h"
#include "kseq.h"
#include "KSeqBufferReader.h"
KSEQ_INIT(kseq_buffer_t*, kseq_buffer_rea... |
35d307f8cc6454d0584a8e945f3323197a79cc53a89355c10f035df680adc95f | C++ | 18,870 | 679 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
b2b04008d16ae94c5031f6231d0152c60fdbf0536d28314a5593d3233a14869d | C++ | 19,222 | 622 | // 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 ... |
5edc1fc4aa2f8c615fe32b495ef78c7e1f0ba39ab987aac03aa3b7fd6ae91581 | C++ | 19,237 | 676 | //
// Copyright (c) 2009-2010 Mikko Mononen memon@inside.org
//
// This software is provided 'as-is', without any express or implied
// warranty. In no event will the authors be held liable for any damages
// arising from the use of this software.
// Permission is granted to anyone to use this software for any purpose... |
6cbc461830a7c73ea5cb78d6ee6c16853441ce2328a02616f9129f02e87b3e02 | C++ | 19,320 | 440 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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, or
* (at your opt... |
1ffadb2c10a3f4edb795c2f7ff7fe6e796be094b017a8364fdfcc01d5565e4d1 | C++ | 19,349 | 477 | // dear imgui: standalone example application for DirectX 12
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// FIXME: 64-bit only for now! (Because sizeof(ImTextureId) == sizeof(void*))
#include "imgui.h"
#include "imgui_impl_win32.h"
#include "imgui_impl_dx12.h"
#i... |
ff743aba04fa32c8013d7a57dc015dab4d5dd011a41a1e192b24a00c807ceba2 | C++ | 19,495 | 565 | extern "C" {
#include <linux/zstd.h>
}
#include <gtest/gtest.h>
#include <memory>
#include <string>
#include <iostream>
using namespace std;
namespace {
struct WorkspaceDeleter {
void *memory;
template <typename T> void operator()(T const *) { free(memory); }
};
std::unique_ptr<ZSTD_CCtx, WorkspaceDeleter>
crea... |
0c5633073598a2636abd0ada420ae576d4c4a9f2981896b4c20e34dad5137945 | C++ | 19,569 | 706 | #include <sys/types.h>
#include <dirent.h>
#include <errno.h>
#include <iostream>
#include <sstream>
#include <fstream>
#include <vector>
#include <utility>
#include <unordered_map>
#include <algorithm>
#include <string>
#include <zlib.h>
#include <cassert>
#include "edit_dist.h"
#include "ssw/ssw_cpp.h"
#include "kseq... |
df0083e05fc1f66b6f0195f0f8b80e4e163c029f97c490f124416f89a68dc071 | C++ | 19,761 | 497 | #include "Sequence.h"
#include "Debug.h"
#include "Util.h"
#include "simd.h"
#include "SubstitutionMatrix.h"
#include "Parameters.h"
#include "MathUtil.h"
#include "SubstitutionMatrixProfileStates.h"
#include "PSSMCalculator.h"
#include "DBReader.h"
#include <climits> // short_max
#include <cstddef>
std::vector<Sequen... |
1b3b11ed26cc26ed8f7404f95536e1882ad3af37dbe41bdd3ceab55cffb597f1 | C++ | 19,766 | 624 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* 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
* ... |
a58a79c8c0fce0107620a4343293e8d0090697e76b0c462ab0cab65c7cb45b84 | C++ | 19,867 | 749 |
#include "stdafx.h"
#include "MdFunc.h"
#include "abi.h"
#include "script_func_impl.h"
#include "window.h"
// internal to this file
struct MdFuncEntry
{
LPCTSTR name;
void *function;
MdType rettype;
MdType argtype[23];
};
#define md_mode decl
#include "lib\functions.h"
#undef md_mode
MdFuncEntry sMdFunc[]
{
... |
6f64307d580d2d8b50a57662e4117185d1aa53094ba31f6519ed311e43130606 | C++ | 19,870 | 459 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
ea15a15094b478de91758e75ecfdbce8ca52486656760bc2f5d8d45c4eb01d9e | C++ | 19,951 | 699 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* 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
* ... |
b4368ce550285a84c550b41ac951f3a9213c13db6f0b671e64dcf680f6c24f4d | C++ | 19,989 | 639 | /*++
Module Name:
BigAlloc.cpp
Abstract:
Allocator that uses big pages where appropriate and possible, and page-aligns in any case to avoid false sharing.
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "Compat.h"
#includ... |
b4c2f071898fd1cc26359fb06d7775e011cd1e06b5ee440af8cafabf40441f9f | C++ | 20,161 | 495 | #include "MsaFilter.h"
#include "Parameters.h"
#include "PSSMCalculator.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "CompressedA3M.h"
#include "MathUtil.h"
#include "AlignmentSymmetry.h"
#include "Matcher.h"
#include "simd.h"
#include "kseq.h"
#include "KSeqBufferReader.h"
KSEQ_INIT(... |
2e39b0f956d9c2a5a06a8c468c864f98ce3505e941d197bf83bb122678307fa2 | C++ | 20,214 | 396 | #include "CacheFriendlyOperations.h"
#include "Util.h"
#include <cmath>
template<unsigned int BINSIZE>
CacheFriendlyOperations<BINSIZE>::CacheFriendlyOperations(size_t maxElement, size_t initBinSize) {
// find nearest upper power of 2^(x)
size_t size = pow(2, ceil(log(maxElement)/log(2)));
size = std::max... |
1aec826d8b48683b6afd298900c2fcf65870ecb7ae3192afb15f9737140b1b97 | C++ | 20,491 | 475 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
3c4e9034a2afe2fc5562d078257584c2415d6e4dbd4720d87744de0b9c172b8a | C++ | 20,699 | 772 | /**
* Copyright 2019-2024, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <fstream>
#include <limits> // for numeric_limits
#include <map>
#include <numeric> // for iota
#include "../../../src/common/io.h"
#include "../../../src/common/json_utils.h"
#include "../../../src/common/threading_utils.h" // ... |
f812723bdfc0f83f18296d08a32ea1c3823853f37e6f30fb482db4ed65b3f52f | C++ | 20,729 | 515 | /**
* Copyright 2020-2025, XGBoost Contributors
*/
#include "quantile.h"
#include <limits>
#include <numeric> // for partial_sum
#include <utility>
#include "../collective/aggregator.h"
#include "../common/error_msg.h" // for InvalidMaxBin
#include "../data/adapter.h"
#include "categorical.h"
#include "hist_util.... |
fe7b3523482dc995473b3ae4cfa88e237fe7ef1838a1dfa1aaab3ba30209b37c | C++ | 20,795 | 482 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
1be583b4b4f3d313d5428d42a6c9550f432bae61fdf77daf47815c207552dacf | C++ | 21,021 | 611 | /*
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under both the BSD-style license (found in the
* LICENSE file in the root directory of this source tree) and the GPLv2 (found
* in the COPYING file in the root directory of this source tree).
*/
#include "plat... |
b6b02ee247f32f9428108bc8a921aa1c164bec91bb9ab416531d8bbb7834d71c | C++ | 21,241 | 795 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
74bd33a12527da01d75b4524d6ea60de9bb5697fc7967b1c3857425dab8512e2 | C++ | 21,443 | 461 | //
// Created by mad on 12/15/15.
#include "UngappedAlignment.h"
UngappedAlignment::UngappedAlignment(const unsigned int maxSeqLen,
BaseMatrix *substitutionMatrix, SequenceLookup *sequenceLookup,
const unsigned char *dbRemap)
: subMatri... |
be13be617028105b9241f2126e6caa3d28a258a5bd0541af2afab1125179293a | C++ | 21,577 | 582 | #include <Python.h> // NOLINT(build/include_alpha)
// Produce deprecation warnings (needs to come before arrayobject.h inclusion).
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <boost/make_shared.hpp>
#include <boost/python.hpp>
#include <boost/python/raw_function.hpp>
#include <boost/python/suite/index... |
9671260feca9fb3da1a654acd1cd6cd854e8b390a85030eb7d72fbdc45adb63c | C++ | 21,709 | 475 | #include "ClusteringAlgorithms.h"
#include "Util.h"
#include "Debug.h"
#include "AlignmentSymmetry.h"
#include "Timer.h"
#include <queue>
#include <algorithm>
#include <climits>
#include <unordered_map>
#include <FastSort.h>
#ifdef OPENMP
#include <omp.h>
#endif
ClusteringAlgorithms::ClusteringAlgorithms(DBReader<DB... |
4c0bba28f3234c518b649e598d787b89454a8d2d28111a023d1ed17259d1a46b | C++ | 21,980 | 605 | //
// caffe_.cpp provides wrappers of the caffe::Solver class, caffe::Net class,
// caffe::Layer class and caffe::Blob class and some caffe::Caffe functions,
// so that one could easily use Caffe from matlab.
// Note that for matlab, we will simply use float as the data type.
// Internally, data is stored with dimensi... |
539b70d4da2372a494c2e3e3c836fae68e5a570a8ce26735b39403d70bedc1d4 | C++ | 22,019 | 687 | /*++
Module Name:
FASTQ.cpp
Abstract:
Fast FASTQ genome "query" reader.
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
This class is NOT thread safe. It's the caller's responsibility to ensure that
at most one thread uses an instance at any time.
Revision History:... |
a9b073663c24990e9a5eeb15312d84a77068674a89b03b7c01aa4a9ae3b361b3 | C++ | 22,033 | 448 | /*++
Module Name:
ChimericPairedEndAligner.cpp
Abstract:
A paired-end aligner calls into a different paired-end aligner, and if
it fails to find an alignment, aligns each of the reads singly. This handles
chimeric reads that would otherwise be unalignable.
Authors:
Bill Bolosky, June, 2013
E... |
f31300eddb58c0d01306db53676cc97d16488b8a5db52161c79b4d384237f6ae | C++ | 22,034 | 533 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
6283663da61a8ed56d1af101b869d68da427a43dd484a41af8e26c74b009ca73 | C++ | 22,038 | 488 | //
// Created by mad on 11/29/16.
//
#include "CSProfile.h"
#include "simd.h"
#include "K4000.crf.h"
ContextLibrary::ContextLibrary(){
std::string lib((const char *)K4000_crf, K4000_crf_len);
read(lib);
}
ContextLibrary *ContextLibrary::contextLibrary = NULL;
ContextLibrary::~ContextLibrary() {
for (si... |
767fddabc1ac15585a1d98252b666e8b646d269740f16cfd7a5ad4cc082851c6 | C++ | 22,123 | 446 | // dear imgui: Platform Binding for Windows (standard windows API for 32 and 64 bits applications)
// This needs to be used along with a Renderer (e.g. DirectX11, OpenGL3, Vulkan..)
// Implemented features:
// [X] Platform: Clipboard support (for Win32 this is actually part of core dear imgui)
// [X] Platform: Mouse... |
0d695fa399db217af7200b120dbdf28e7310bc909a8bdf591b44b55498d9346f | C++ | 22,259 | 911 | #include <sstream>
#include "emitterutils.h"
#include "indentation.h" // IWYU pragma: keep
#include "yaml-cpp/emitter.h"
#include "yaml-cpp/emitterdef.h"
#include "yaml-cpp/emittermanip.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
namespace YAML {
class Binary;
struct _Null;
Emitter::Emitter() : m_pSta... |
d683db8b379303fe3cdc1e2d2a04b3a7a46db9c528d1927a9a1eda9f02a0f241 | C++ | 22,294 | 479 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "IndexReader.h"
#include "MemoryMapped.h"
#include "NcbiTaxonomy.h"
#include "MappingReader.h"
#include "algorithm"
#include <iterator>
#include <map>
#ifdef OPENMP
#include <omp.h>
#e... |
b22275d2f8f7ce79d5e457e6658c03874e6411e939706160baeb515b15ffcb84 | C++ | 22,313 | 436 | //
// Created by Martin Steinegger on 2019-01-04.
//
#include "QueryMatcher.h"
#include "PrefilteringIndexReader.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "Command.h"
#include "kmersearch.h"
#include "Debug.h"
#include "LinsearchIndexReader.h"
#include "Timer.... |
9f325a09296e65529c2d71b9339e077265c3c9966defadc3ad10836ccbf1e5aa | C++ | 22,548 | 476 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "FileUtil.h"
#include "Util.h"
#include "BacktraceTranslator.h"
#include "EvalueComputation.h"
#include "CompressedA3M.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#include "MultipleAlignment.h"
#include "MsaFilt... |
163a31b6ea48b779ca93a832a6ad800abafa5bafc4bc3c594f3183e9f6d260f1 | C++ | 23,033 | 569 | #include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/cudnn_deconv_layer.hpp"
#include "caffe/layers/deconv_layer.hpp"
#include "caffe/test/test_caffe_main.hpp"
#include "caffe/test/test_gradient_check_util.hpp"
namespace ... |
b4ff75ac834375ef75bdf7259e1758e641862932bb8667f9d304066939f2f27b | C++ | 23,107 | 714 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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, or
* (at your opt... |
ba39f7f079404140cb878b6d62e6de6f344ee1e31738c1b17596900ff734b01b | C++ | 23,129 | 473 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
cfb460de7fd025de1b9c41e083003896038c2a525c5697fb2389c81b841e8ce0 | C++ | 23,177 | 662 | // 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 ... |
41da153f7b04e8f13f078217c6735da61a6ba5fbbb5988f6128f8a9b21bf81d3 | C++ | 23,224 | 500 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Orf.h"
#include "AlignmentSymmetry.h"
#include "Timer.h"
#include "IndexReader.h"
#include "FileUtil.h"
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
void chainAlignme... |
be53fa63625e4bb962bcbe8e600dffc20f0a81ca9f66436269559c8d353d3418 | C++ | 23,311 | 205 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* 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
* ... |
5f96545c22baa785a8f899cae450b87f05c3ae81ee67e3382a635f0ec81375b8 | C++ | 23,330 | 568 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#include "FileUtil.h"
#include "ExpressionParser.h"
#include "FastSort.h"
#include <fstream>
#include <random>
#include <iostream>
#include <unordered_map>
#include <sstream>
#include <regex.h>
#ifdef OPENMP
#incl... |
6959c49b6c515ed557812c153a9b27deb72f33e3e0240ac48e49880354567460 | C++ | 23,460 | 882 | /*************************************************************************//**
*
* @file single and pairwise reading of sequences from FASTA/FASTQ files
*
* (c) 2017-2023 André Müller (mail@andremueller-online.de)
* MIT License
*
***************************************************************************... |
03f3f2dad8f517179fe522a694994a6beaa3acb41733462bb17d10a5a8fdcd1e | C++ | 23,486 | 849 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
4d8690eb9a0f48cfc1646bbdb040ae918889b9f6a061e25892d083e423a30617 | C++ | 23,725 | 475 | #include "DistanceCalculator.h"
#include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "QueryMatcher.h"
// #include "CovSeqidQscPercMinDiag.lib.h"
// #include "CovSeqidQscPercMinDiagTargetCov.lib.h"
#include "QueryMatcher.h"
#include "Nucle... |
0d2bfc9e775663fe36401e9e96490ccfd16a4d278bdfae81b6bc5abbdcb1c6f1 | C++ | 23,751 | 543 | // dear imgui: standalone example application for SDL2 + Vulkan
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// Important note to the reader who wish to integrate imgui_impl_vulkan.cpp/.h in their own engine/app.
// - Common ImGui_ImplVulkan_XXX functions and stru... |
b3135893c5e05f54b006560fad6cfa1a9e25abc24f97a18f6a0f934ecf1534d3 | C++ | 23,764 | 334 | #include "Util.h"
#include "Parameters.h"
#include "Debug.h"
#include "FileUtil.h"
#include "CommandCaller.h"
#include "DownloadDatabase.h"
#include <cassert>
#include "databases.sh.h"
extern bool hide_base_downloads;
extern std::vector<DatabaseDownload> externalDownloads;
std::vector<DatabaseDownload> downloads = {{... |
07376011e1244bba3107511a304b1188bb5eba8af1cc08e36cb00baa93bcd367 | C++ | 23,851 | 542 | // dear imgui: standalone example application for Glfw + Vulkan
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// Important note to the reader who wish to integrate imgui_impl_vulkan.cpp/.h in their own engine/app.
// - Common ImGui_ImplVulkan_XXX functions and stru... |
7b09eef2ea589ebb960b844764afa49185fdba8f97c8850281ebe0e45e08a70f | C++ | 23,854 | 612 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
32014bdec4e32f164aaf7b024fcf6db032963698040d3a48c58a9eadef0fee69 | C++ | 23,953 | 708 | // 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 ... |
a5aa691cac2665ba44b27a6634b5a50fdcc7bb7fd9194ad03fce97346b9d4aa4 | C++ | 23,991 | 993 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
084a9413f27ea3890ffbea4d30b01964185b40fb88bc2f29f3830063a6d16a49 | C++ | 24,023 | 802 | /*
* Copyright (C) 2019-2024 Matthias Klumpp <matthias@tenstral.net>
*
* Licensed under the GNU Lesser General Public License Version 3
*
* This program 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 Founda... |
43726d4cad9db2c40b3e7f4081bc1c433d65c56fc3b02f290bccfb213641d903 | C++ | 24,036 | 581 | /**
* Copyright 2017-2025, XGBoost Contributors
* \file updater_quantile_hist.cc
* \brief use quantized feature values to construct a tree
* \author Philip Cho, Tianqi Checn, Egor Smirnov
*/
#include <algorithm> // for max, copy, transform
#include <cstddef> // for size_t
#include <cstdint> // for uint32_t,... |
d3f289f83a182ae088ef1ca58e1e7a496574d4af963a826e88af14c5ba1773fd | C++ | 24,155 | 846 | /******************************************************************
* *
* Copyright by Joachim Saul <saul@gfz-potsdam.de> *
* *
***********************************************... |
9ad159190293bc1da5f4e6b5b3c8c216a83c57498dd0070f808c5546435bb388 | C++ | 24,237 | 536 | // dear imgui: Renderer for DirectX10
// This needs to be used along with a Platform Binding (e.g. Win32)
// Implemented features:
// [X] Renderer: User texture binding. Use 'ID3D10ShaderResourceView*' as ImTextureID. Read the FAQ about ImTextureID!
// [X] Renderer: Support for large meshes (64k+ vertices) with 16-b... |
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