sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d19d4949f1a381ea33a721595b1d1badc30fc97289035572b3c40e6ba9776159 | C++ | 24,586 | 699 | // 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 ... |
23ad046b1973462a1bc2eb91ab8ec0121ae4d022dd25afe7f55961a17308059d | C++ | 24,690 | 711 | /**
* Copyright 2019-2025, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/c_api.h>
#include <xgboost/data.h>
#include <xgboost/json.h> // Json
#include <xgboost/learner.h>
#include <xgboost/version_config.h>
#include <algorithm> // for copy_n
#include <array> // for array
#include <cstdd... |
eb6ebed09d735ee342b6b1b070b78db1830f0a6f69cb82cf931fa20c3f932fa9 | C++ | 24,697 | 618 | /**
* Copyright 2018-2023 by Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/base.h> // for bst_node_t, bst_bin_t, Gradient...
#include <xgboost/context.h> // for Context
#include <xgboost/data.h> // for BatchIterator, BatchSet, DMatrix
#include <xgboost/host_devic... |
9635a51193a81a83d747ff5ae46d2ebaf9b113d00da012db7cd588df1ed2c1eb | C++ | 24,861 | 645 | /**
* Copyright 2020-2024 by XGBoost contributors
*/
#include <gtest/gtest.h>
#include <oneapi/dpl/random>
#include "../../../plugin/sycl/tree/hist_updater.h"
#include "../../../plugin/sycl/device_manager.h"
#include "../../../src/tree/common_row_partitioner.h"
#include "../helpers.h"
namespace xgboost::sycl::tr... |
2fc9a0325a191f5b2bd17dab1b5645f0274ac780162623f0a748a44ad1660c20 | C++ | 24,944 | 609 | /**
* Copyright 2014-2024, XGBoost Contributors
* \file updater_colmaker.cc
* \brief use columnwise update to construct a tree
* \author Tianqi Chen
*/
#include <algorithm>
#include <cmath>
#include <vector>
#include "../common/error_msg.h" // for NoCategorical
#include "../common/random.h"
#include "sample_posi... |
e280b299541d9005de58f339f42943a5408f863c3fd7f9624c58b2cb581ec6ed | C++ | 25,256 | 710 | ///////////////////////////////////////////////////////////////////////////////
//
// AutoIt
//
// Copyright (C)1999-2007:
// - Jonathan Bennett <jon@hiddensoft.com>
// - Others listed at http://www.autoitscript.com/autoit3/docs/credits.htm
// - Chris Mallett (support@autohotkey.com): adaptation of this file's
/... |
78b25f224cbf73ffccfb04513da2952ded5704058503bdc154edf8d8667520cb | C++ | 25,339 | 654 | #include "BlockAligner.h"
#include "Sequence.h"
#include "Util.h"
#include "Parameters.h"
#include "SubstitutionMatrix.h"
#include "EvalueComputation.h"
#include "DistanceCalculator.h"
#define MAX_SIZE 4096 //change
#define MIN_SIZE 32
#include <algorithm>
BlockAligner::BlockAligner(
int dbtype,
size_t maxSe... |
51c2be4683c5c07e6e0feb0b175899d3d8dfb58c7dd5286ca10063f16e1ef4f1 | C++ | 25,369 | 767 | #include "stdafx.h"
#include "Compat.h"
#include "LandauVishkin.h"
#include "mapq.h"
#include "Read.h"
#include "BaseAligner.h"
#include "Bam.h"
#include "exit.h"
#include "Error.h"
using std::make_pair;
using std::min;
LandauVishkinWithCigar::LandauVishkinWithCigar()
{
for (int i = 0; i < MAX_K+1; i++) {
... |
a612f76becdbe506f84739ee9b6f5ec7ae8588412bec8b5f6683adce5b17d2f4 | C++ | 25,968 | 785 | /*
* 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... |
07e738a04cfd1a4b1c66a0bbc55d9dfa6cba8a34ca4a0d97711c1f407f666719 | C++ | 25,975 | 725 | /**
* Copyright 2016-2025, XGBoost contributors
*/
#include "helpers.h"
#include "../../src/data/batch_utils.h" // for AutoHostRatio
#include <gtest/gtest.h>
#include <xgboost/gbm.h>
#include <xgboost/json.h>
#include <xgboost/learner.h>
#include <xgboost/logging.h>
#include <xgboost/metric.h>
#include <xgboost/ob... |
1b55b32c5d08b38c40b24d8ff9863575a04eb65a42f60ee00cb7487e30d4e75b | C++ | 25,990 | 987 | /**
* Copyright 2019-2024, XGBoost Contributors
*/
#include "xgboost/json.h"
#include <array> // for array
#include <cctype> // for isdigit
#include <cmath> // for isinf, isnan
#include <cstdint> // for uint8_t, int16_t, int32_t, int64_t
#include <cstdio> // fo... |
2ff5b9fc114e642842be4cb88cf620136ceb2dc8421ea75489ba6a470694f415 | C++ | 26,039 | 802 | /*++
Module Name:
Geonome.cpp
Abstract:
Genome class for the SNAP sequencer
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
Revision History:
Adapted from Matei Zaharia's Scala implementation.
--*/
#include "stdafx.h"
#include "Genome.h"
#include "GenericFile.h"
#incl... |
6737eb005150a7d0fcba2d6e20f70df924ec8b113342410ead402c6bdbfd656b | C++ | 26,043 | 742 | #include "Util.h"
#include "Debug.h"
#include "FileUtil.h"
#include "BaseMatrix.h"
#include "SubstitutionMatrix.h"
#include "Sequence.h"
#include "Parameters.h"
#include <sys/resource.h>
#include "itoa.h"
#include <unistd.h>
#ifdef __APPLE__
#include <sys/param.h>
#include <sys/sysctl.h>
#endif
#include "simd.h"
#inc... |
2dc85a0cfca41aea0bb7b62fad08d37cab7987a4f0ad51a05fc6e0572e125ed8 | C++ | 26,078 | 1,038 | #include "yaml-cpp/emitterstyle.h"
#include "yaml-cpp/eventhandler.h"
#include "yaml-cpp/yaml.h" // IWYU pragma: keep
#include "gtest/gtest.h"
namespace YAML {
namespace {
class NullEventHandler : public EventHandler {
virtual void OnDocumentStart(const Mark&) {}
virtual void OnDocumentEnd() {}
virtual void O... |
9d1b8b5bc8bfb61eb3e193ebc640d28665de86aa1d4aeb0e93ca065ce4f992e7 | C++ | 26,149 | 551 | // dear imgui: Renderer for DirectX11
// This needs to be used along with a Platform Binding (e.g. Win32)
// Implemented features:
// [X] Renderer: User texture binding. Use 'ID3D11ShaderResourceView*' as ImTextureID. Read the FAQ about ImTextureID!
// [X] Renderer: Support for large meshes (64k+ vertices) with 16-b... |
6d4d76d2bdb1afde9d30ea327bba098dd3d27447f5a6c7421a2aa8331d6546c6 | C++ | 26,602 | 519 | #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 "NucleotideMatrix.h"
#include "ReducedMatrix.h"
#include "ExtendedSubstitutionMatrix.h"
#include "IndexReader.h"
#include "Fast... |
5764f6938f34fd977a63c21103ebdd5245e96c5d798a2b0b6c590af783abf909 | C++ | 26,806 | 754 | /**
* Copyright 2019-2024, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h>
#include <xgboost/host_device_vector.h> // for HostDeviceVector
#include <xgboost/json.h> // for Json, Object
#include <xgboost/learner.h> // for Learner
#include <limits> // for nu... |
eeaea96f4fa76305d6fe4b70e2de8ad2784040ce238543a0ce080be931acf089 | C++ | 26,860 | 658 | // Created by: Yang Zhang
// Description: Python bindings for all actions in the library
// Functionality:
// 1. frame_voxelize: Voxelization of a single frame
// 2. frame_observation: Compute the observable for a single frame
// 3. marching_observer: Marching observer algorithm for a slice of frames/trajectory
// 4. d... |
1fc7ce59ab264b70278e21ccd684ecc848152b03b3934bbcdc67716b16ac2327 | C++ | 27,024 | 743 | /*++
Module Name:
ReadSupplierQueue.cpp
Abstract:
Code for parallel queue of reads
Authors:
Bill Bolosky, November, 2012
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "Read.h"
#include "Compat.h"
#include "ReadSupplierQueue.h"
#include "exit.h"
#include ... |
dd40c1582e6a35e31ff46f9264266d184f21326a5288ed6d12a337d3dea0b167 | C++ | 27,244 | 758 | /**
* Copyright (c) 2019-2023, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/base.h>
#include <xgboost/data.h>
#include <xgboost/feature_map.h> // for FeatureMap
#include <xgboost/json.h>
#include <xgboost/learner.h>
#include <string>
#include "../../src/common/io.h"
#include "../../src/common... |
4c5ee3a2e8ddf5651877b02bd7a36dfcb7f96c7e0633001b1fa2b0e12ab37f00 | C++ | 27,377 | 586 | #include "MsaFilter.h"
#include "Parameters.h"
#include "PSSMCalculator.h"
#include "IndexReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "DBConcat.h"
#include "HeaderSummarizer.h"
#include "CompressedA3M.h"
#ifdef OPENMP
#include <omp.h>
#endif
int result2msa(int argc, const char **argv... |
d7922ac8717625bb967005439ddf034ceca1249c30e1cee41a51d7c8fd46d6b1 | C++ | 27,574 | 693 | /**
* Copyright 2023-2025, XGBoost contributors
*/
#include "lambdarank_obj.h"
#include <dmlc/registry.h> // for DMLC_REGISTRY_FILE_TAG
#include <algorithm> // for transform, copy, fill_n, min, max
#include <cmath> // for pow, log2
#include <cstddef> // for size_t
#include <cstdint> // for int3... |
4c13d30f4d99e42a64eaaa4a0f75a3cc52a53f8f51fbe0cefc41f4918173abc5 | C++ | 27,625 | 909 | #include "../core/types.h"
#include "../core/maths.h"
#include "../core/platform.h"
#include "../core/mesh.h"
#include "../core/voxelize.h"
#include "../core/sdf.h"
#include "../core/pfm.h"
#include "../core/tga.h"
#include "../core/perlin.h"
#include "../core/convex.h"
#include "../core/cloth.h"
#include "../external/... |
5a49e38ae672bc042243284682ccfa706d71e2667705b38e305f2f17e838232b | C++ | 27,974 | 794 | /*
coding=utf-8
Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required ... |
9cf2e6edc1d5c40a2a20d1b071481d3290e7939d7a9a6b5876d914db77a0d1b9 | C++ | 28,011 | 601 | #include "Alignment.h"
#include "Util.h"
#include "Debug.h"
#include "Matcher.h"
#include "QueryMatcher.h"
#include "DBWriter.h"
#include "IndexReader.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "SubstitutionMatrixProfileStates.h"
#include "FileUtil.h"
#include "Parameters.h"
#include "Fas... |
e8362bfbd10d5105322ef8d5a90fbdb573a8ec647bb54698120cf112817ece59 | C++ | 28,090 | 626 | #include "PrefilteringIndexReader.h"
#include "DBWriter.h"
#include "Prefiltering.h"
#include "ExtendedSubstitutionMatrix.h"
#include "FileUtil.h"
#include "IndexBuilder.h"
#include "Parameters.h"
extern const char* index_version_compatible;
unsigned int PrefilteringIndexReader::VERSION = 0;
unsigned int PrefilteringI... |
762963ab1a0e68158a2320b2b6a013c4592a47c7f19353fa451c5d2fd4ef16f7 | C++ | 28,135 | 915 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* detrend.cpp
*
* Code generation for function 'detrend'
*
*/
/* Include files */
#include "detrend.h"
#incl... |
f907fa5db3ae32b9fe4429aa96bf524c266e2885256fe9f6969dbcf8deeb78e4 | C++ | 28,652 | 791 | /*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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 option... |
4da59cb2d264425963dcea201117d6a6e213418d4a1fe775000fa4485cb65d34 | C++ | 28,675 | 663 | //
// Created by mad on 2/3/16.
//
#include <Debug.h>
#include <Util.h>
#include "MsaFilter.h"
#include "simd.h"
#include "MathUtil.h"
#include "MultipleAlignment.h"
MsaFilter::MsaFilter(int maxSeqLen, int maxSetSize, SubstitutionMatrix *m, int gapOpen, int gapExtend) :
// TODO allow changing these?
PLTY_GAPO... |
8f11ad3640ff49c5983db7e797297176f4aa59032efdb5f080adb416fa5ce3b9 | C++ | 28,782 | 955 | #include "Character.h"
#include "BVH.h"
#include "DARTHelper.h"
#include "Muscle.h"
#include <tinyxml2.h>
using namespace dart;
using namespace dart::dynamics;
using namespace MASS;
typedef tinyxml2::XMLElement TiXmlElement;
typedef tinyxml2::XMLDocument TiXmlDocument;
Character::
Character()
: mSkeleton(nullptr), ... |
63b1bb4922f7f0dbc285e8f1d2699c4dd37ebb5a62d75335d2f7c9170f5f0a95 | C++ | 29,021 | 827 | #include "NcbiTaxonomy.h"
#include "FileUtil.h"
#include "MathUtil.h"
#include "Debug.h"
#include "Util.h"
#include "sys/mman.h"
#include <fstream>
#include <algorithm>
#include <cassert>
const int NcbiTaxonomy::SERIALIZATION_VERSION = 2;
int **makeMatrix(size_t maxNodes) {
size_t dimension = maxNo... |
6c398eac93d18c441a3f78c2269e7abd7845a21b4294c24b540fce6bbb87023a | C++ | 29,048 | 748 | #include "utilities.h"
#include <Rcpp.h>
#include <algorithm>
#define _USE_MATH_DEFINES
#include <cmath>
#include <iterator> // std::ostream_iterator
#include <sstream> //std::stringstream
#include <unordered_map>
#include "KDTreeVectorOfVectorsAdaptor.h"
#include "nanoflann.h"
#define KNN_K 5
namespace miic {
... |
6f2a33e5752c1c4db0bf9e2015c6f28abf1b083de3ed7777510eb030394a61e1 | C++ | 29,299 | 673 | // dear imgui: Renderer for DirectX12
// This needs to be used along with a Platform Binding (e.g. Win32)
// Implemented features:
// [X] Renderer: User texture binding. Use 'D3D12_GPU_DESCRIPTOR_HANDLE' as ImTextureID. Read the FAQ about ImTextureID!
// [X] Renderer: Support for large meshes (64k+ vertices) with 16... |
05ebd82cb2612cfd4c94fc8f6f6291c0a167a5cd5f74d837169b2457272d7756 | C++ | 29,399 | 748 | #include "DBWriter.h"
#include "DBReader.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "Concat.h"
#include "itoa.h"
#include "Timer.h"
#include "Parameters.h"
#define SIMDE_ENABLE_NATIVE_ALIASES
#include <simde/simde-common.h>
#include <cstdlib>
#include <cstdio>
#include <sstream>
#include <... |
4afed28d66d269ba651bbd7d48946345d532af80a5ea6aa6b1acb498924e8c2f | C++ | 29,857 | 927 | /*
* Copyright 2017-2018, Florian Breitwieser
*
* This file was originally developed for the KrakenUniq taxonomic classification system.
*/
#include "hyperloglogplus.h"
#include <stdio.h>
#include<cassert>
#include<vector>
#include<stdexcept>
#include<iostream>
#include<fstream>
#include<cmath> //log and sqrt... |
9dc3f02b0da1286768ad41b83c846672da3c4c1b1d675f2a8af9b358b32b881a | C++ | 29,970 | 864 | /*
*
* Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
* 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 above ... |
355cd17fa73250981652174e3ad82a510aea4be8e38f21c8d54da9a7d7c44d1e | C++ | 30,309 | 916 | /*
* 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... |
1a21a4dd7945b005f47b5f96fda4fdbc90be42fde2582deca23633eee3d5092f | C++ | 30,330 | 837 | /**
* Copyright 2017-2024, XGBoost contributors
*/
#include <gmock/gmock.h>
#include <gtest/gtest.h>
#include <xgboost/learner.h> // for Learner
#include <xgboost/logging.h> // for LogCheck_NE, CHECK_NE, LogCheck_EQ
#include <xgboost/objective.h> // for ObjFunction
#include <xgboost/version_conf... |
1960fa0a111e9650a9f7060d2dffa17b46a4a468d9a0329e7e42747bcc630715 | C++ | 30,761 | 638 | #include "SubstitutionMatrix.h"
#include "QueryMatcher.h"
#include "FastSort.h"
#include "Util.h"
#define FE_1(WHAT, X) WHAT(X)
#define FE_2(WHAT, X, ...) WHAT(X)FE_1(WHAT, __VA_ARGS__)
#define FE_3(WHAT, X, ...) WHAT(X)FE_2(WHAT, __VA_ARGS__)
#define FE_4(WHAT, X, ...) WHAT(X)FE_3(WHAT, __VA_ARGS__)
#define FE_5(WHAT... |
e7e7ba75f72b982a26f76a69368306f34013aa1e20893f7e302e035e07c90c86 | C++ | 30,789 | 823 | // 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 ... |
344ce26fa0362ad092fd98db1b57b5b72e77fd06a4748dbaf8cf9318b2443e7b | C++ | 31,070 | 664 | #include "Util.h"
#include "Parameters.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "MemoryMapped.h"
#include "Alignment.h"
#include "itoa.h"
#include "Timer.h"
#include <algorithm>
#include <map>
#include <unordered_set>
#inclu... |
b673e408f03cdcdbf02b560cb4d6a9785ea223bdabda3296ed34a7ec976d3f30 | C++ | 31,591 | 941 | /*
* 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... |
bfabc67d0d1fd66f0cd383a97ec950eb014a7de859edeef6a9a24e83209e8ad8 | C++ | 31,692 | 804 | /*++
Module Name:
AlignerContext.cpp
Abstract:
Common parameters for running single & paired alignment.
Authors:
Ravi Pandya, May, 2012
Environment:
User mode service.
Revision History:
Integrated from SingleAligner.cpp & PairedAligner.cpp
--*/
#include "stdafx.h"
#include "Compat.h"
#i... |
4c81475e86a7e1e04aa9d2abf4d2f4007b004ae78ad0acb527036cf992a41035 | C++ | 31,777 | 1,025 | /*++
Module Name:
DataWriter.cpp
Abstract:
General file writer.
Environment:
User mode service.
Not thread safe.
--*/
#include "stdafx.h"
#include "BigAlloc.h"
#include "Compat.h"
#include "DataWriter.h"
#include "ParallelTask.h"
#include "exit.h"
#include "Bam.h"
#include "Error.h"
using std:... |
786dddf4fac9c9bff5b05f754631cda9017c1d4bc2d81fd44b0f89f61333fed1 | C++ | 31,792 | 883 | /*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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 versio... |
9627739f16af10a8600848e17cd18e4234d4b2b90c322ce934c679ce93703db0 | C++ | 32,074 | 738 | /*++
Module Name:
ReadWriter.cpp
Abstract:
General file writer.
Environment:
User mode service.
Not thread safe.
--*/
#include "stdafx.h"
#include "BigAlloc.h"
#include "Compat.h"
#include "Read.h"
#include "SAM.h"
#include "Tables.h"
#include "RangeSplitter.h"
#include "ParallelTask.h"
#includ... |
b08bd96b2c26d1e2002b572b7d92162c5c33d85976e2ed637ffa64254d7e0932 | C++ | 32,308 | 636 | #include "DBReader.h"
#include "CommandCaller.h"
#include "Util.h"
#include "FileUtil.h"
#include "Debug.h"
#include "PrefilteringIndexReader.h"
#include "searchtargetprofile.sh.h"
#include "searchslicedtargetprofile.sh.h"
#include "blastpgp.sh.h"
#include "translated_search.sh.h"
#include "blastp.sh.h"
#include "blast... |
6058966065db54750263e2548511c45c595a0dd27705c32d151f76788d69d007 | C++ | 32,710 | 688 | // dear imgui: Renderer for modern OpenGL with shaders / programmatic pipeline
// - Desktop GL: 2.x 3.x 4.x
// - Embedded GL: ES 2.0 (WebGL 1.0), ES 3.0 (WebGL 2.0)
// This needs to be used along with a Platform Binding (e.g. GLFW, SDL, Win32, custom..)
// Implemented features:
// [X] Renderer: User texture binding. ... |
357133ec81be2d786402320e58a6ebe335840b4a89e45e41e0c02687ec16f223 | C++ | 33,076 | 680 | // dear imgui: wrapper to use FreeType (instead of stb_truetype)
// Get latest version at https://github.com/ocornut/imgui/tree/master/misc/freetype
// Original code by @vuhdo (Aleksei Skriabin). Improvements by @mikesart. Maintained and v0.60+ by @ocornut.
// Changelog:
// - v0.50: (2017/08/16) imported from https://... |
ce98f1241faca02a41ce8d03b6cb871641b4f3be1e8ae45137d1c9e7e59908ce | C++ | 33,106 | 1,062 | // 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 ... |
7157240515eabdc3d34de4f52f8e83c90818dd817d2ded96d71957086ffdc591 | C++ | 33,121 | 849 | /*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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 option... |
f98ff4ec9194a1625eb075fd371f86b178be68945da17eac0eb91a66d69c2803 | C++ | 33,143 | 1,036 | #include "GLfunctions.h"
#include <assimp/cimport.h>
#include <iostream>
#include <GL/gl.h>
#include <GL/glu.h>
#include "GL/glut.h"
#define USE_VNORMAL 0
#define RESOLUTION 16
static GLUquadricObj *quadObj;
static void initQuadObj(void)
{
quadObj = gluNewQuadric();
if (!quadObj)
// DART modified erro... |
e26165e2dc4114a12ba83a8315e5e74413beff521aa0f305bd2b7d94cbdc0923 | C++ | 33,496 | 704 | //
// Created by mad on 3/24/15.
//
#include "PSSMCalculator.h"
#include "simd.h"
#include "MathUtil.h"
#include "BaseMatrix.h"
#include "Sequence.h"
#include "Util.h"
#include "Debug.h"
#include "MultipleAlignment.h"
PSSMCalculator::PSSMCalculator(SubstitutionMatrix *subMat, size_t maxSeqLength, size_t maxSetSize, in... |
cbea5142ec70670df3e9a6115dcd950fa925737007bc714a1146a88000eea5e9 | C++ | 33,633 | 850 | /*
* Copyright 2013, Daehwan Kim <infphilo@gmail.com>
*
* 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 opti... |
960d21eee9d067b54d2037bb4b1a1231425a261598ba62436d22a9aeeeba1261 | C++ | 34,342 | 884 | /*!
* Copyright 2017-2024 by Contributors
* \file hist_updater.cc
*/
#include "hist_updater.h"
#include <oneapi/dpl/random>
#include <functional>
#include "../../src/tree/common_row_partitioner.h"
#include "../common/hist_util.h"
#include "../../src/collective/allreduce.h"
namespace xgboost {
namespace sycl {
... |
4d4471ce26e9d44dbcc8052f60598505518ca477f8ddde8ef67f58a62ab1b64a | C++ | 34,628 | 759 | //
// Created by Martin Steinegger on 17.09.18.
//
#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 "NucleotideMatrix.h"
#include "FastSort.h"
#include "SubstitutionMatrixProf... |
8afc36a5b51acd54edea03d40f4e171372bf8656b73925b18d39e676f06d2354 | C++ | 35,009 | 889 | /**
* Copyright 2020-2025, XGBoost Contributors
*/
#include "test_predictor.h"
#include <gtest/gtest.h>
#include <xgboost/context.h> // for Context
#include <xgboost/data.h> // for DMatrix, BatchIterator, BatchSet, MetaInfo
#include <xgboost/host_device_vector.h> // for HostDeviceVector
#... |
4c1512d1cf287f611f3dc4d720ff810abd35671d5af5bae3a122130856512b46 | C++ | 35,047 | 752 | /*
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... |
35622fa7b23a672e7447cfe794d2bf4f4851791d89e9666a31a3f94bc1eee16c | C++ | 35,075 | 1,654 | /* $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 Copyri... |
c8580fbb77ea5b1551d1d707413d991aec517c875f0438d8c948de5d13dac240 | C++ | 35,897 | 848 | /*
* createdb
* written by Martin Steinegger <martin.steinegger@snu.ac.kr>.
* modified by Maria Hauser <mhauser@genzentrum.lmu.de> (splitting into sequences/headers databases)
* modified by Milot Mirdita <milot@mirdita.de>
*/
#include "FileUtil.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include... |
1ff880d856eb428e65fc6711f846ee59ee2a07cfbbabc91d31ea60b3fe138964 | C++ | 35,949 | 1,209 | #include "stdafx.h"
#include "TextIO.h"
#include "script.h"
#include "script_object.h"
#include "script_func_impl.h"
EXTERN_SCRIPT;
UINT g_ACP = GetACP(); // Requires a reboot to change.
#define INVALID_CHAR UorA(0xFFFD, '?')
#ifndef UNICODE
CPINFO GetACPInfo()
{
CPINFO info;
GetCPInfo(CP_ACP, &info);
return info... |
678ffea9339c44d3b213691ddf990d5bf1a18cd0ce297d330c9225492ce48c3b | C++ | 37,227 | 910 | /*
* 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... |
ede21cd1d649997dc8055e5b484625d678ce9a962315f02fc422b201650c8da6 | C++ | 37,342 | 774 | /*
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... |
416add00e09fb893193d26bb0aeb9e02e35c736572d55752390ec6b61b462094 | C++ | 38,696 | 1,055 | // 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 ... |
70b0c0d92626a5fe4e1871dfe92ecf5b011dc24185aefb4cf4bc80220a1f8b7e | C++ | 38,861 | 1,131 | #include "specexamples.h"
#include "yaml-cpp/yaml.h" // IWYU pragma: keep
#include "gtest/gtest.h"
#define EXPECT_THROW_PARSER_EXCEPTION(statement, message) \
ASSERT_THROW(statement, ParserException); \
try { \
statement; ... |
39419cbd2feb5fa112309b544ba9fda95ef12f65b5be646052b9498fc5f172e3 | C++ | 39,555 | 1,043 | /**
* Copyright 2014-2025, XGBoost Contributors
*
* \file gbtree.cc
* \brief gradient boosted tree implementation.
* \author Tianqi Chen
*/
#include "gbtree.h"
#include <dmlc/omp.h>
#include <dmlc/parameter.h>
#include <algorithm> // for equal
#include <cstdint> // for uint32_t
#include <memory>
#include <s... |
99b989ba23ca51510bf4859cd87c6c754f20af10a520de9ed6ec0b2ccdab0960 | C++ | 39,672 | 994 | #include <algorithm>
#include <map>
#include <set>
#include <string>
#include <utility>
#include <vector>
#ifdef USE_HDF5
#include "hdf5.h"
#endif // USE_HDF5
#include "caffe/common.hpp"
#include "caffe/layer.hpp"
#include "caffe/net.hpp"
#include "caffe/parallel.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caff... |
262f305de8f280d7e6117977b94097323dfdbd33dea8d9b57a8168b21b9ef0b0 | C++ | 39,719 | 1,070 | /*
* 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... |
af4de6d874c21d2453f2dca817bf6a9ea51e733ee64069ea7d1887457f8a11e9 | C++ | 40,343 | 1,092 | /*
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... |
607f0b7e2ed10e3349ce224ce7a13b899859db415ea2e490f4d728bdcc130179 | C++ | 40,501 | 1,304 | // 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 ... |
3588aef74758d140e3102caafe3a37490c2b2a9691021bffc764b4c963a4ee5b | C++ | 40,650 | 1,081 | #include <algorithm>
#include <vector>
#include "google/protobuf/text_format.h"
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/absval_layer.hpp"
#include "caffe/layers/bnll_layer.hpp"
#include "caffe/layers/clip_layer.hpp"
#include "c... |
e84bfd9cdbf22d50ac6c921171815f29ccce47957f2982c877a093caba24e14f | C++ | 40,940 | 1,228 | // 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 ... |
13f97f2e0c315fa44f2a05274fc30085759179e3025de3da9266b108789f23d8 | C++ | 41,494 | 1,128 | #include "stdafx.h"
#include "Compat.h"
#include "AffineGapVectorized.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
// #define TRACE_AG 1
AffineGapVectorizedWithCigar::AffineGapVectorizedWithCi... |
b2a72e7f506933b332b43a3187a2854e1d9f4721918cb8e417d3fa5326913823 | C++ | 41,651 | 1,245 | /*
* 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... |
8a7048edb6e4fda9c041667aed159d209ca69d467079dd543f0e5aecff652bf7 | C++ | 42,345 | 1,286 | // 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 ... |
cc61385443186c612a170d187d976d9eadaa27b462828396c075b236c11d40a9 | C++ | 42,985 | 1,259 | // 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 ... |
81da18022e6024404d6f15de8ce3454449e175da086b79e8680c233a85cde6e4 | C++ | 42,998 | 1,169 | #include "DBReader.h"
#include "FastSort.h"
#include <algorithm>
#include <climits>
#include <cstring>
#include <cstddef>
#include <random>
#include <sys/mman.h>
#include <sys/stat.h>
#include <fcntl.h>
#include "MemoryMapped.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "itoa.h"
#ifdef OPE... |
b27a4eccb3450b33135aedcee5a1dc21a21457f85152a0267615aa955342fd4d | C++ | 43,012 | 1,461 | /*
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... |
e37cdd0740bdcfecf9fbdd7a151f42a07e21fd1edc1ae7471d959f6f5a4d4560 | C++ | 43,497 | 1,127 | #include <google/protobuf/io/coded_stream.h>
#include <google/protobuf/io/zero_copy_stream_impl.h>
#include <google/protobuf/text_format.h>
#include <boost/filesystem.hpp>
#include <map>
#include <string>
#include "caffe/common.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caffe/util/io.hpp"
#include "caffe/util/... |
a6ad3a443dfae73bd7a066b49756f7aedc4d3758b3f7c0691c20b887af0eacf8 | C++ | 44,049 | 1,086 | #include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/conv_layer.hpp"
#ifdef USE_CUDNN
#include "caffe/layers/cudnn_conv_layer.hpp"
#endif
#include "caffe/test/test_caffe_main.hpp"
#include "caffe/test/test_gradient_check_... |
0df3dd1867b7e89b634f2db164e9070744325a8e260e3407de12fde53ef0424a | C++ | 44,110 | 1,058 | /*++
Module Name:
PairedAligner.cpp
Abstract:
Functions for running the paired end aligner sub-program.
Authors:
Matei Zaharia, February, 2012
Environment:
User mode service.
Revision History:
Adapted from cSNAP, which was in turn adapted from the scala prototype
--*/
//
// TODO: This i... |
814ce5883ee4bf64ad9b6eab5a9b9ca5ad997b13874406a819062dd3128ace7e | C++ | 44,630 | 1,450 | /*++
Module Name:
SortedDataWriter.cpp
Abstract:
File writer that sorts records using a temporary file.
Environment:
User mode service.
Not thread safe.
--*/
#include "stdafx.h"
#include "BigAlloc.h"
#include "Compat.h"
#include "Util.h"
#include "DataWriter.h"
#include "BufferedAsync.h"
#inclu... |
ba19d4c1479b69fb80bfb91b7d3e1d7c06bb2e3124fd3c0e8676c0316c2647b0 | C++ | 44,997 | 1,427 | // 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 ... |
186b5c7d2cb00dcacb6de41ae34f18fb2e71eb3c2a330ad4a9c290f881f32d81 | C++ | 45,165 | 1,289 | #include <algorithm>
#include <string>
#include <utility>
#include <vector>
#include "google/protobuf/text_format.h"
#include "gtest/gtest.h"
#include "caffe/common.hpp"
#include "caffe/parallel.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caffe/sgd_solvers.hpp"
#include "caffe/util/io.hpp"
#include "caffe/test... |
a575ae25a5cc91124c09e5c3a0c9db7ddccbfea820b4aa71bfde1dfd6c5698a2 | C++ | 45,293 | 1,411 | // 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 ... |
4886d765e1a3a98a59475fd78cfe04ca30c73088806f9c528d2eccef29c208e8 | C++ | 45,541 | 1,605 | #include "Parameters.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "MemoryMapped.h"
#include "FastSort.h"
#include <dirent.h>
#ifdef OPENMP
#include <omp.h>
#endif
static uint32_t be32(const unsigned char *p) {
uint32_t v = ((uint32_t)p[0] << 24) | ((uint32_t)p[1] <... |
c19932e739554758304ea0e95a9da2ee9bfbcb0bc607073e32ffa2ffcc0cfec0 | C++ | 45,798 | 1,400 | /*
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... |
3c81a036b738a9cbd92c1e6f568ef413522e1d8134ecad616f02c689d9d7f770 | C++ | 45,982 | 1,069 | /**
* Copyright 2017-2025, XGBoost Contributors
*/
#include <algorithm> // for max, fill, min
#include <any> // for any, any_cast
#include <cassert> // for assert
#include <cstddef> // for size_t
#include <cstdint> // for uint32_t, int32_t, uint64_t
#include <memory> // for unique_ptr, shared_ptr... |
88a44b67cd3e8381a84ec0223637c15aa28c7c92ac0fce906794cab1ad569a0c | C++ | 46,398 | 1,135 | #include "kraken2_data.h"
#include "reports.h"
#include "taxonomy.h"
#include <algorithm>
#include <assert.h>
#include <atomic>
#include <cstdlib>
#include <cstring>
#include <err.h>
#include <functional>
#include <limits>
#include <sstream>
#include <string.h>
#include <unistd.h>
#include <unordered_map>
#include <ve... |
e76eb3d5e1a8a006d8cc2ff204fc8c17b1ed2b88230794d4e600bb35b1b42fd4 | C++ | 46,714 | 1,157 | /*
* Copyright 2013, Daehwan Kim <infphilo@gmail.com>
*
* 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 opti... |
e4a715ff340591ea7699a7f8870dd524e74f589038b53ac951ba4651d5f71266 | C++ | 46,739 | 873 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "IndexReader.h"
#include "FileUtil.h"
#include "TranslateNucl.h"
#include "Sequence.h"
#include "Orf.h"
#include "MemoryMapped.h"
#include "NcbiTaxonomy.h"
#include "MappingReader.h"
#... |
d999310a89d5969d30b0ee8a0bb88f29397d10f19b268fedb32baed7172fa1c7 | C++ | 47,425 | 1,799 | /*
* 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... |
ab233af3dbcd728697d4e4626cbe48dee8e46726bd2861404fd5dfe6488e5cce | C++ | 48,306 | 1,416 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include <err.h>
#include <sys/wait.h>
#include <sys/types.h>
#include "kraken2_headers.h"
#include "kv_store.h"
#include "taxonomy.h"
#include "seqreader.h"
#include "fast_... |
4f34b0ad2365175fe5070e5592a57d143b4206a950979e5b0265def7c53f4721 | C++ | 48,631 | 1,590 | /*
* 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
* ... |
23b9e4e093f54c3d13ca6336222766df907b26c3e232e240ca49e77e6899707e | C++ | 49,842 | 1,307 | /**
* Copyright 2015-2024, XGBoost Contributors
* \file tree_model.cc
* \brief model structure for tree
*/
#include <dmlc/json.h>
#include <dmlc/registry.h>
#include <xgboost/json.h>
#include <xgboost/tree_model.h>
#include <cmath>
#include <iomanip>
#include <limits>
#include <sstream>
#include <type_traits> // ... |
74cce9838c909c1aeda3353804b0c73cb5d2f9cbde74584b4ffbc21a6c35ad0a | C++ | 50,942 | 1,342 | // 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 ... |
0b4beda988f4d012fcc1ddb4d8b3548916aeb757b9887273ef0bcf0e98bb9c30 | C++ | 51,036 | 1,190 | #include "Fwbw.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "IndexReader.h"
#include "SubstitutionMatrix.h"
#include "Alignment.h"
#include "Matcher.h"
#include "Util.h"
#include "Parameters.h"
#include "simd.h"
#include "Sequence.h"
#include "Timer.h"
#include <iostream>
#include <algori... |
2f6195173bfac3f75d9cb54264550694878ac218223a804aeec409dba2b1359b | C++ | 51,129 | 862 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <string.h>
#include <cmath>
#include "PSSMCalculator.h"
#include "Sequence.h"
#include "Indexer.h"
#include "ExtendedSubstitutionMatrix.h"
#include "SubstitutionM... |
8dc9e37dda1e8d6ce11a36c219fe66a4bd4f3519f58da8e04081e0ecc1e07107 | C++ | 51,677 | 1,327 | #include "LambdaCalculation.h"
#include "Debug.h"
#include <algorithm>
#include <cmath>
#include <cstdlib>
#include <limits>
#include <map>
#include <numeric>
#include <vector>
#include <random>
#define LambdaCalculation_DEBUG 0
struct LambdaCalculationConstants {
static constexpr double MATRIX_SINGULARITY_THRESH... |
09cfa72cd36889bd58b60f2afa9f33d5502c3eb4148d779bae04a63a50dcece2 | C++ | 51,816 | 1,029 | #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 "IndexReader.h"
#include "FastSort.h"
#include "BlockAligner.h"
#include "Alignment.h"
#include "AlignmentSymmetry.h"
#include ... |
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