sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3fc9064b4484a6b04c571aa1652faa0b77ec1a9e44da484d4b0175ceec23c6b1 | C | 7,842 | 242 | /*
Written by Ruibin Xi
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <ctype.h>
#include <time.h>
#include <sys/time.h>
#include "../lib/read.h"
#include <getopt.h>
#include <math.h>
#include <unistd.h>
#include "ITree.h"
typedef struct args_countRead_t{
FILE *rea... |
339798a528348f3b27ca6d2a13c7e86d3c9a83f6d4dc39e81a5c0c8c5e26f0a7 | C | 7,848 | 198 | /*************************************************
* Perl-Compatible Regular Expressions *
*************************************************/
/* This file contains character tables that are used when no external tables
are passed to PCRE by the application that calls it. The tables are used only
for charact... |
71e8aacca5991f6909bffa163417dd1facfb59e226d61f462dbbfc359626d521 | C | 7,929 | 241 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
53a6ec779050b87092bf679f509f39268c8f51f51a6b3c6873f42035d3c0fa94 | C | 8,031 | 260 | /*
* Copyright (c) 2017-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).
* You may select,... |
abb035cce76f3ba665b4f433ff36ae9dc99585e6f50d3bcd8a5aadad3b4aaccb | C | 8,056 | 333 | /*
* 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... |
5521169ff964e1b9535b762c1893f006d54e55d53a546cb5f31b64765c7d3718 | C | 8,097 | 213 | /**
* Copyright 2019-2023 by XGBoost contributors
*
* \file c-api-demo.c
* \brief A simple example of using xgboost C API.
*/
#include <assert.h>
#include <stddef.h>
#include <stdint.h> /* uint32_t,uint64_t */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <xgboost/c_api.h>
#define safe_xgbo... |
2d5c2cec300d961f9a86e8591b55d2f4ce0e5bbda50b60b5e89a5e0de3adba07 | C | 8,126 | 319 | #include "utils.h"
#include "number.h"
#include "fml.h"
#include "fastq.h"
#include "htslib/thread_pool.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include <zlib.h>
KSEQ_INIT(gzFile, gzread)
static int usage()
{
fprintf(stderr, "assem in.fq\n");
fprintf(stderr, " -t Threads.\n");
fpri... |
6d478555cbf5ec3fec1328790395215edbdda742f98833c84c7e87cc1cc2e6de | C | 8,231 | 149 | #include "utils.h"
#include "version.h"
#include "pisa_version.h"
#include <string.h>
int usage()
{
fprintf(stderr, "\n\x1b[1mPISA\x1b[0m - a collection of tools for single cell data pre-processing and interpretation.\n");
fprintf(stderr, "Version: %s + htslib: %s\n", PISA_VERSION, HTS_VERSION_TEXT);
fprint... |
62abed5895582b11e8905df7e9325cab9960e14cac47eb01c9f0a5b19d78c7eb | C | 8,544 | 203 | /* ******************************************************************
hist : Histogram functions
part of Finite State Entropy project
Copyright (C) 2013-present, Yann Collet.
BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
Redistribution and use in source and binary forms, wit... |
3b3f44e71fe9a48eca4f95687c73e6d9ddc364758f3c796bfeed034fc9039aa4 | C | 8,616 | 333 | /*
Copyright (C) 2016,2017 BGI Research
Author: Shi Quan (shiquan@genomics.cn)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limita... |
4c08d219fe7ed275ad224e5f1d8eb84a64363b01940002690d7ecd71c564ab65 | C | 8,630 | 259 |
/* timeBEPeriod( BE , ms )
* [ BE , ms ] = timeBEPeriod
*
* MEX wrapper for Windows system calls timeBeginPeriod and timeEndPeriod.
* These can be used to request higher precision timers for the calling
* process.
*
* Input argument BE is a scalar char. If it is 'b' then timeBeginPeriod
* is used. O... |
2a4df22380cc7f5760ab62a0a31b01fe7937685ab0c66622efb8a9d310b2408e | C | 8,699 | 217 | #include <stdio.h>
#include <string.h>
#include "block_aligner.h"
// max block size, assume that two seqs will not have a larger gap than this
#define MAX_SIZE 4096
// threshold number of iterations where the score does not change for terminating alignment
#define ITER 2
// compute traceback, which is slightly slowe... |
90da6fcef4dfd36096a5e88f37c5b980cb220071ab760e873a1c824c1d492ca5 | C | 8,748 | 353 | #include "dict.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include <zlib.h>
typedef struct dict_val {
int idx;
int ref;
} dict_val_t;
KHASH_MAP_INIT_STR(name, dict_val_t)
KSTREAM_INIT(gzFile, gzread, 8193)
struct dict {
int n, m;
char **name;
kh_name_t ... |
4fdbfc06cad63b038f2c725be268b015baca41705ae3dcbf478e22a3c0607a0a | C | 8,754 | 352 | #include "dict.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include <zlib.h>
typedef struct dict_val {
int idx;
int ref;
} dict_val_t;
KHASH_MAP_INIT_STR(name, dict_val_t)
KSTREAM_INIT(gzFile, gzread, 8193)
struct dict {
int n, m;
char **name;
kh_name_t ... |
0ac9d8b07b74c27bbca27c4be4d53c095fef93426c38848f6711a679224b750f | C | 8,834 | 242 | /*
* Copyright (c) 2008 Yuta Mori All Rights Reserved.
* 2011 Attractive Chaos <attractor@live.co.uk>
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restr... |
3a6db6d07df28532920bf64f7a02b86f57ea610db7cc747a238643d69c6984d9 | C | 8,845 | 344 | /*
Copyright (C) 2016,2017 BGI Research
Author: Shi Quan (shiquan@genomics.cn)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limita... |
84185f56d5fd2c34dd7108793801c4d5cc563a7291e2469d0433329bc4363baf | C | 8,869 | 240 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
59d438b332563376a4465ebf8de4fde3610004143720182b9bd6fb47c043aeca | C | 8,883 | 288 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
2e7c9184d16d3c00168b335fbecba704d4db54dcd22a6a61dde3a9ac7aead80e | C | 8,950 | 339 | #include "udf.h"
#include "mem.h"
#include "stdio.h"
#include "stdlib.h"
#include "time.h"
#define C0 0.154
#define C1 1.9
#define C2 2.1
#define C4 0.88
#define rho 998.2
#define D0 0.00001003
#define SC 0.9
#define alpha_max 600000 /*900000*/
DEFINE_DIFFUSIVITY(Diff,c,t,i)
{
real De;
real D... |
c6d7b1a29b325110d5ee99cf4aebd54a8cd1ac2b0d1b86c222cddf524f5e6b7a | C | 9,002 | 295 | /*
* Copyright (c) 2000-2008 Marc Alexander Lehmann <schmorp@schmorp.de>
*
* Redistribution and use in source and binary forms, with or without modifica-
* tion, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
ef93a5858ae0ff3c455994d156eed86a31b359192d2c747be288cf25497e9e8f | C | 9,185 | 155 | /* Copyright (c) 2015 by Contributors
*
* This file was initially generated using the following R command:
* tools::package_native_routine_registration_skeleton('.', con = 'src/init.c', character_only = F)
* and edited to conform to xgboost C linter requirements. For details, see
* https://cran.r-project.org/doc/m... |
7d0d66cf8de3419564dffbcc5058d782a071f91859ac73a00b3d7a979b9ac42d | C | 9,243 | 329 | #include "dna_pool.h"
#include "htslib/kstring.h"
static const unsigned char seq_nt16_table[256] = {
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /... |
15d99972073dad90c08a74f5d7504d70d7af0019d4a4eccbf8929a5ed261430b | C | 9,248 | 283 | /* The MIT License
Copyright (C) 2010, 2013-2014 Genome Research Ltd.
Copyright (C) 2011 Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software wit... |
edb4d763af13f5d447cd09c463fbb321753456ff637f63bfc5d12a90a27bd392 | C | 9,253 | 277 | /*
* Stack-less Just-In-Time compiler
*
* Copyright 2009-2012 Zoltan Herczeg (hzmester@freemail.hu). 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 ... |
e695587b3e4ce0f74b864b983d0587fc9c2386f371e38634825e4b9accbafd83 | C | 9,404 | 274 | /**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"... |
cc8351c2e3ed8a019e22dc0856f981e955c4c96ef5acbd8b75c3d35d7130a33f | C | 9,428 | 263 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
fe88069224e5053747225b85cd532c52d34c00eb80088c4b1fcd30d1ff6cd416 | C | 9,487 | 271 | // Annotate bed files with GTF annotation.
// Required a 6-column bed file, with format as "chr, start, end, name, score, strand".
// Annotated tags such as genes and functional region will be put into extra columns,
// therefore the output file is not exactly a formal bed file; the format of output file is
// "chr, st... |
b940c4313dd2436a63ed873126fb68e25a14033af38d7b66d401e14ee385d7cc | C | 9,554 | 236 | /*
Common functions of New Generation Entropy library
Copyright (C) 2016, Yann Collet.
BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
m... |
a0c37b93fc957b9465c6d8bc467a77671b3ece54bde97c72b937ff86f3be27a7 | C | 9,560 | 335 | #ifdef _OPENMP
#include <omp.h>
#endif
#include<R.h>
#include<Rdefines.h>
#include <Matrix.h>
extern int *random_idx(const int n);
extern int shuffle(double tmp[], int const idx[], const int n);
SEXP association_test1(SEXP A, SEXP B, SEXP C, SEXP _W, SEXP _perm, SEXP return_arr)
{
int n_perm = asInteger(_perm);
... |
b2ceacdab4201d4f61600f11829f6159ff6b39cf2f36f9737576de259404105d | C | 9,570 | 225 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
a804c35a93d3eeae4354af7b8b936faa83462d0a8e0020970f2bc49dc8b7a756 | C | 9,607 | 329 | /* htsfile.c -- file identifier and minimal viewer.
Copyright (C) 2014-2019 Genome Research Ltd.
Author: John Marshall <jm18@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Softwar... |
d3c18abd95ec868b0edd21edec246da5e3895df5342108c791e76e93646cb570 | C | 9,627 | 308 | #define eps 2.2204460492503131e-16
#define doublemax 1e50
#define INF 2e50
#define listINF 2.345e50
#ifndef min
#define min(a,b) ((a) < (b) ? (a): (b))
#endif
#ifndef max
#define max(a,b) ((a) > (b) ? (a): (b))
#endif
/* Find minimum value of an array and return its index */
int minarray(doub... |
8e03aaa00b35676d0c5457aa4bfec3fb6d8fccc37953fb7a4be8be17cab6f7c1 | C | 9,630 | 312 | #include "utils.h"
#include "htslib/sam.h"
#include "coverage.h"
#include "bed.h"
#include "number.h"
#ifdef _OPENMP
#include <omp.h>
#endif
static struct args {
const char *input_fname;
const char *output_fname;
const char *bc_list;
const char *tag;
const char *umi_tag;
struct dict *barcodes;... |
f4688aeb5e6f60d34d934173d7c379fe84edfd0fa5b13237da4c70332fb90b0e | C | 9,631 | 357 | #include "utils.h"
#include "dict.h"
#include "htslib/thread_pool.h"
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "htslib/kstring.h"
#include "number.h"
static struct args {
const char *input_fname;
const char *output_fname;
const char *report_fname;
int file_thread;
int keep_dup;... |
eb9f7db649b14e2005bdca6a065954760fb1f5e2e2c7fe2a92287f07206fb945 | C | 9,729 | 332 | #include <R.h>
#include <Rdefines.h>
#include <Rinternals.h>
#include <string.h>
#include "utils.h"
#include "htslib/sam.h"
#include "htslib/hts.h"
#include "htslib/bgzf.h"
#include "htslib/tbx.h"
#include "htslib/kstring.h"
#include "coverage.h"
#include "dict.h"
SEXP depth2matrix(SEXP _fname, SEXP _name, SEXP _star... |
f89d8531ca584ccc496366a2a11de992ce05090e53cadcb3822fd6fd33fd71e7 | C | 9,730 | 368 | /*written by Ruibin Xi April 26 2010*/
#include "pos_cnt_lst.h"
static COUNT_LST_NODE cnt_node_create(int read_count);
/*creat a new node of type COUNT_LST_NODE given a read_count at certain position*/
static POS_LST_NODE pos_node_create(int pos, int read_cnt);
static void LST_add(LST lst, int pos, int read_cnt);
st... |
bb574a799f8cf9fcaeaeb202dab5247f349569dd46eedbc09d0e6e0f37afbce3 | C | 9,918 | 310 | /**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"... |
3d2ffd7f6e0eb35d374620b184f59bfbcafca4c5263ac38eb3c73a476ab7f09d | C | 10,021 | 424 | /* The MIT License
Copyright (C) 2011 by Attractive Chaos <attractor@live.co.uk>
Copyright (C) 2013-2018 Genome Research Ltd.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software withou... |
0648da0c676f7a1602046e802916fc57546edfc9998c6e6971541899902803d0 | C | 10,131 | 299 | /*************************************************
* Perl-Compatible Regular Expressions *
*************************************************/
/* PCRE is a library of functions to support regular expressions whose syntax
and semantics are as close as possible to those of the Perl 5 language.
... |
ac7f5dbc0322776db1f7c591236d9a9dfdf7818d2323722f76832e8911142d12 | C | 10,229 | 378 | #include "utils.h"
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "htslib/kstring.h"
#include "dict.h"
#include "bed.h"
#include "region_index.h"
#include "number.h"
#include "pisa_version.h"
#ifdef _OPENMP
#include <omp.h>
#endif
static struct args {
const char *input_fname;
const char *bed_fname;
... |
0bc114471610d7c375adc6310e41686ded1124cea350cee15deaef091b7377e4 | C | 10,386 | 321 | /*
Written by Ruibin Xi
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <ctype.h>
#include <time.h>
#include <sys/time.h>
#include "../lib/read.h"
#include "../lib/gamma.h"
#include <getopt.h>
#include <math.h>
#include <unistd.h>
static int HghLevelBinCount = 100; /*For com... |
7b08f32e9f30ee1d11ae6cbe7d79bef62d15b8d89db72d0f7f6579110d37745e | C | 10,475 | 432 | /*
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public
* License v2 as published by the Free Software Foundation.
*
* This program is distributed in the hope that it will be us... |
9be391b16fb7b6c9676dabac497496eac7f3f53a474a7836329ff78abfaff834 | C | 10,616 | 445 | #include "utils.h"
#include "htslib/khash.h"
#include "htslib/kstring.h"
#include "sim_search.h"
#define BASE_TERM 0x0
#define BASE_A 0x1
#define BASE_C 0x2
#define BASE_G 0x3
#define BASE_T 0x4
#define BASE_N 0x5
//static int kmer_min = 5;
static int kmer_max = 21;
static int kmer_size = 5;
typedef struct ss_... |
92e7da9aeb572bdf9885ace5b66819558062e98d583efd3a2f8ec3eeca27a43d | C | 10,640 | 401 | #include "utils.h"
#include "number.h"
#include "htslib/kstring.h"
SEXP parse_var_names(SEXP name)
{
int l = Rf_length(name);
SEXP sl = PROTECT(allocVector(VECSXP, 5));
SEXP chr = PROTECT(allocVector(STRSXP, l));
SEXP start = PROTECT(allocVector(INTSXP, l));
SEXP ref = PROTECT(allocVector(STRSXP, ... |
efeb27120383b8a9b817dbe8c7f3a86ffb72bc6f6abe6c6fdafec68825e094b4 | C | 10,713 | 448 | /* textutils.c -- non-bioinformatics utility routines for text etc.
Copyright (C) 2016, 2018-2019 Genome Research Ltd.
Author: John Marshall <jm18@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), ... |
d604c6badd66303a2b6e0c81c60cfa80f79c7ddb16b5c1ddccff23ea2880da86 | C | 10,750 | 254 | /* fitblk.c contains minimal changes required to be compiled with zlibWrapper:
* - #include "zlib.h" was changed to #include "zstd_zlibwrapper.h"
* - writing block to stdout was disabled */
/* fitblk.c: example of fitting compressed output to a specified size
Not copyrighted -- provided t... |
9f1f0dfdc3bcf8876214ff3b9d2c52a022ae39da1bab6105ac8f6b60e756aa54 | C | 10,769 | 366 | /*
* Copyright (c) 2017-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 <std... |
5b23ed2215907a69acd66df7a1377e6e8d9b6df611d544a9b98e27ebdc0f83d9 | C | 10,909 | 332 | /*
* FSE : Finite State Entropy decoder
* Copyright (C) 2013-2015, Yann Collet.
*
* BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
... |
131e56f996ad3227632cc656eccadb352c2a2a160b7d830df540cccf80deeec2 | C | 10,951 | 340 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
9759747705f1dc9344cdc7e954b8dc2158ccf887cb1a9bdfce63d45aeaab63c4 | C | 10,955 | 422 | /*
Title: Read Illumina Barcode
Author: Alexandre Schoepfer
Version: 28rd July 2021, 10:15 (GMT+1)
Notes:
*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#define NOT_FOUND 0
#define FOUND 1
#define LOW_QUALITY 2
#define WRONG_SIZE 3
unsigned long lookupTableLength = 0;
unsigned long dataLength = 0... |
557cd621ebc3776773290f027d63ad564803cb118d24c370b1cc1bd874c4095c | C | 11,057 | 362 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
5c668d5353627f450af6286b205c9b879f736dce24e3662a5eca1bb41fbe8db0 | C | 11,065 | 381 | // gene_fusion.c -- intepret gene fusions based on UMI tagged cDNA library.
//
//
#include "utils.h"
#include "htslib/sam.h"
#include "htslib/kstring.h"
#include "number.h"
#include "dict.h"
static struct args {
const char *input_fname;
int qual_thres;
const char *gene_tag;
const char *cell_tag;
co... |
b288251a1cb24fbc069375ccdbe2e87d73f68be8b3a75f8fb7230199665fd157 | C | 11,088 | 432 | /*
* 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... |
d3e03bd0fdc0228861873c6165cb1fd7e2775f1545ae334a78fb2978ae66b385 | C | 11,172 | 355 | /*
* 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.
*
* qr.c
*
* Code generation for function 'qr'
*
*/
/* Include files */
#include "qr.h"
#include "eml_int_forl... |
70ee245827e72d7e94f67d14403e376446a81177e9c3ce1f9d59a1459acfc343 | C | 11,179 | 309 | /* ******************************************************************
FSE : Finite State Entropy decoder
Copyright (C) 2013-2015, Yann Collet.
BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
Redistribution and use in source and binary forms, with or without
modification, are p... |
00dbed8d15a08249d18dfddcd9cf64f3a8330736b1312b5d46326d38fe82cb0b | C | 11,485 | 401 | /*
Copyright (C) 2016,2017 BGI Research
Author: Shi Quan (shiquan@genomics.cn)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limita... |
eb28ca6ecf4d7c4e96e197502a1bfde0c89e016b4cc9f23e65770527febfa6d1 | C | 11,661 | 284 | #include <stdio.h> /* fprintf */
#include <stdlib.h> /* malloc, free, qsort */
#include <string.h> /* strcmp, strlen */
#include <errno.h> /* errno */
#include <ctype.h>
#include "io.h"
#include "fileio.h" /* stdinmark, stdoutmark, ZSTD_EXTENSION */
#include "platform.h" /* Large Files support */
#inclu... |
f026c1464b04682c46377c2a1508b18f4bccc3c0bc0c3c02e671a50c4e61fd2e | C | 11,748 | 290 | /* realn.c -- BAQ calculation and realignment.
Copyright (C) 2009-2011, 2014-2016, 2018 Genome Research Ltd.
Portions copyright (C) 2009-2011 Broad Institute.
Author: Heng Li <lh3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated d... |
4687fea6053f3145e724a3a239f7e851a701067c68338c670cf1c63cb05ee23b | C | 11,772 | 404 | // Count all reads and reads with predefined tag for each cell barcode in the bam file
#include "utils.h"
#include "number.h"
#include "htslib/khash.h"
#include "htslib/kstring.h"
#include "htslib/sam.h"
#include "htslib/kseq.h"
#include "dict.h"
#include <zlib.h>
#include "biostring.h"
#include "read_anno.h"
static s... |
5db0b964ad4cb338d29e6917bfb41433b53efd07f327079856da0fb3d67a9fdb | C | 11,994 | 455 | /*
Title: Parse PacBio Alignement main
Author: Alexandre Schoepfer
Version: 28th July 2021, 10:15 (GMT+1)
Notes: - TODO: memory allocation checks
- TODO: dynamic memory for parseCS
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include "libsccod... |
5abc4088d4a6b1b647b5d180ee448bf5ad2afca1768cb69d9e424f2a03110ecc | C | 12,014 | 400 | /*
* 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.
*
* sum.c
*
* Code generation for function 'sum'
*
*/
/* Include files */
#include "sum.h"
#include "eml_int_f... |
a2934f6599d5d195c492ef0933979cd3c118cf55fcaa8e51d5667adcea3256dc | C | 12,262 | 312 | /* The MIT License
Copyright (C) 2003-2006, 2008-2010 by Heng Li <lh3lh3@live.co.uk>
Copyright (C) 2016-2017 Genome Research Ltd.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software wi... |
6d5d8182454ecf41a4eb465eda47fbc40e8acd3e4df8fc48f4a66a0a5b09147a | C | 12,271 | 426 | /* Copyright (c) 2009 the authors listed at the following URL, and/or
the authors of referenced articles or incorporated external code:
http://en.literateprograms.org/Red-black_tree_(C)?action=history&offset=20090121005050
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software an... |
9d25065060492914bae7daeb459d71a7042c56c20bebdfe5148d7713ac122737 | C | 12,539 | 432 | #include "utils.h"
#include "htslib/sam.h"
#include "htslib/hts.h"
#include "htslib/kstring.h"
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "dict.h"
#include "number.h"
#include "region_index.h"
#include "bed.h"
#include "bam_region.h"
// TN5 offsett
// reads aligning to the + strand were offset by +4 bps... |
735ddcf58a64c15b01068c97c22bd76e2fb800210fde03fed44eb70e5c85f3de | C | 12,747 | 454 | #include "bin.h"
static double lambda = 1;
static double N = 0.0,logN = 0.0; /*total number of reads and log total number of reads*/
static int num_sample=1; /*number of samples*/
static int flag_BIC_diff = 1; /*flag if it's the first time to call the function BIC_diff*/
static bin_list * bin_from_array(double *lin... |
4f41dafc8f0f28a3341d0699d120d9038f6765efcc7610bb6b5046dcaebd088f | C | 12,978 | 500 | /*
* xxHash - Extremely Fast Hash algorithm
* Copyright (C) 2012-2016, Yann Collet.
*
* BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:... |
d7deebd14e809c57ce737dbf4a5a594c6e2ff73c93fd08c560d564fe99c4885d | C | 13,059 | 343 | #include "mex.h"
#include "math.h"
/* RK4 is a function which performs one step of the Runge-Kutta 4 ray tracing
*
* EndPoint = RK4(StartPoint, GradientVolume, StepSize);
*
* inputs :
* StartPoint: 2D or 3D location in vectorfield
* GradientVolume: Vectorfield
* Stepsize : The stepsize
*
* outp... |
10ceb44e7d5572c639a25333e2578e7631b5f427265348de731d6f1c3715e267 | C | 13,184 | 419 | #include "utils.h"
#include "htslib/sam.h"
#include "htslib/kstring.h"
#include "dict.h"
#include "number.h"
#include "bed.h"
#include "coverage.h"
const static int ws1m = 1000000;
static struct args {
const char *input_fname;
const char *output_fname;
const char *bc_list;
const char *tag; // cell bar... |
ef8af3c43623c7a204cd384ff5a2422e1021822e1da033bae39fbaf1f7570a4a | C | 13,326 | 369 | /*
* 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.
*
* _coder_multitaper_spectrogram_coder_api.c
*
* Code generation for function '_coder_multitaper_spectrogram_cod... |
677ea4ed6fc7f8da555d8bff659f552a76c18ecee0be662a6c0790cd51214af9 | C | 13,437 | 396 | /*
Copyright (c) 2015, 2018-2019 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
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 copyright notice,
th... |
7628fe76409c474618998c38419730130c90db090cab90798cd3d80331da25fa | C | 13,500 | 458 | #include "utils.h"
#include "fastq.h"
#include "number.h"
#include "dict.h"
#include "fastq.h"
#include "read_tags.h"
#include "htslib/thread_pool.h"
/*
#ifdef _OPENMP
#include <omp.h>
#endif
*/
static struct args {
const char *input_fname;
const char *output_fname;
const char *report_fname;
const char ... |
f7af2f04198de56258749fb62a17580e06f4b5db61d75a6cfe7322b921b53a1b | C | 13,996 | 437 | /*
Author: James Bonfield
Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL
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 copyright notice,
th... |
c1b951c54181ab85131dc38511f9cac8a5c690141d5edaf45d70adf06f51bb19 | C | 14,148 | 467 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <math.h>
#include <time.h>
#include <getopt.h>
#include "../lib//read.h"
#include "pos_cnt_lst.h"
#define GAP_ERROR 2
static int min_dist_to_gap = 1000000;
static int tt_read_mp = 0; /*total reads processed on the mappable position... |
be41e0fca3780505640b03d1b969a2b3e1414e58a9f45d795a5b25e2d7dcb06a | C | 14,358 | 443 | /*
* 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.
*
* multitaper_spectrogram_coder_emxutil.c
*
* Code generation for function 'multitaper_spectrogram_coder_emxutil... |
1d17109e9fa66fca6d526682d2db498d2fc82d20b8bbc37d5be81040f2944880 | C | 14,616 | 462 | /* tbx.c -- tabix API functions.
Copyright (C) 2009, 2010, 2012-2015, 2017-2019 Genome Research Ltd.
Copyright (C) 2010-2012 Broad Institute.
Author: Heng Li <lh3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation file... |
d8432be186d2ccc69b0f1b19ad63ab1db44b7d3d8beafa11db647cb556d8ec75 | C | 14,672 | 517 | /*
* Stack-less Just-In-Time compiler
*
* Copyright 2009-2012 Zoltan Herczeg (hzmester@freemail.hu). 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 ... |
92d5d813e344fcc25505c99946db79eb24503299eb19e7530e7a0162b8febbe7 | C | 14,684 | 534 | #include <R.h>
#include <Rdefines.h>
#include <Rinternals.h>
#include <Matrix.h>
#include "utils.h"
#include "dict.h"
#include "perm.h"
#include "variant_type.h"
#include "htslib/kstring.h"
#include "htslib/hts.h"
#include "htslib/vcf.h"
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "htslib/faidx.h"
SEXP v... |
8ec28145eb6c0b8b08e7c71149801e62723f42f9a1e788d2ebaa655d50b222a0 | C | 15,107 | 428 | #include "utils.h"
#include "coverage.h"
#include "bed.h"
struct depth *depth_init()
{
struct depth *d = malloc(sizeof(*d));
if (d == NULL) error("Failed to allocate memory.");
memset(d, 0, sizeof(*d));
d->id = -1;
return d;
}
void depth_destroy(struct depth *d)
{
for (;d;) {
struct dep... |
4bc819287a3475e30366a9b439ecae4b66548cf657347fa59e378b354ee7dec8 | C | 15,193 | 546 | #ifdef _OPENMP
#include <omp.h>
#endif
#include<R.h>
#include<Rdefines.h>
#include <Matrix.h>
#include <assert.h>
#define CACHE_PER_BATCH 10000
#define MIN_HIT 1
extern int *random_idx(const int n);
extern int shuffle(double tmp[], int const idx[], const int n);
double *sp_colsums(CHM_SP A, Rboolean mn)
{
dou... |
be3e1ef8101a0ddb21769b0a4afa9f12e926039b8c446aa4c4ef3eab9c3859f2 | C | 15,329 | 440 | #ifdef _OPENMP
#include <omp.h>
#endif
#include<R.h>
#include<Rdefines.h>
#include <Matrix.h>
extern int *random_idx(const int n);
extern int shuffle(double tmp[], int const idx[], const int n);
extern void smooth_W(double * const a, double *s, const int N, CHM_SP W);
struct val {
int v1; // feature
int v2;... |
b76891623a31f1957f8693e9e4ca9ac2ea5dac8cb1d246cdde26d8dc17be8f19 | C | 15,495 | 640 | /* minigzip.c contains minimal changes required to be compiled with zlibWrapper:
* - #include "zlib.h" was changed to #include "zstd_zlibwrapper.h" */
/* minigzip.c -- simulate gzip using the zlib compression library
* Copyright (C) 1995-2006, 2010, 2011 Jean-loup Gailly.
* For conditions of distribution and... |
1e16dbac4fad141b8e061b1ff68c8862da45bda2a9b6f3cf0e6d52114a93bfe6 | C | 15,524 | 464 | /*
* Copyright (c) 2017-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).
* You may select,... |
660ad1e4998bf1604da1eed166c2673c97d6d24917ad89bbde665643bf419225 | C | 15,526 | 422 | /* bgzip.c -- Block compression/decompression utility.
Copyright (C) 2008, 2009 Broad Institute / Massachusetts Institute of Technology
Copyright (C) 2010, 2013-2019 Genome Research Ltd.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentat... |
d2367d1728758afbe17c80cac9d8f4bf1854b299da26757a008090e3912e43f6 | C | 15,779 | 442 | #include <stdio.h> /* fprintf */
#include <stdlib.h> /* malloc, free, qsort */
#include <string.h> /* strcmp, strlen */
#include <errno.h> /* errno */
#include <ctype.h>
#include <time.h>
#include "random.h"
#include "dictBuilder.h"
#include "zstd_internal.h" /* includes zstd.h */
#include "io.h"
#include "util.h... |
55aa3e1389111772e951d530acc9d9568e23957ec7d2f42e179d9fbd3bbcdfd6 | C | 15,897 | 371 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
3923b923a08f375027d94fcd96f2ad38f79068192f37824f0562adce53e281b5 | C | 16,215 | 617 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
3a473ff676555c24f9c480da860973c0fa22ae590c1d5ef415f8bff9698bf4dc | C | 16,286 | 590 | #include <assert.h>
#include <err.h>
#include <strings.h>
#include "blast_defline.h"
#include "blast_utils.h"
asn1_t *init_asn1(const char *filename, uint32_t *block_lens, uint32_t num_oids) {
asn1_t *asn1 = alloc_memory(NULL, sizeof(asn1_t), 0, 1);
asn1->asn1_file = open_file(filename, "r");
asn1->buffer = NUL... |
773bec541ea8358a969f389f7176853296756ea2e271d0583666a685c5eb9088 | C | 16,500 | 671 |
#include "gamma.h"
static void gser(double *gamser, const double a, const double x, double *gln);
static void gcf(double *gammcf, const double a, const double x, double *gln);
static double betacf(const double a, const double b, const double x);
double gammln(const double xx)
{ int j;
double x,y,tmp,ser;
stati... |
1de368d854938a30e34a7a2d2c40dc5d3bbda921789fde88b20a908e3999c441 | C | 17,239 | 668 | /*
Copyright (c) 2005-2006, 2008-2009, 2013, 2015, 2017-2019 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
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 th... |
9480dd570daea2d27ddf7fa0265744b33213b9a04e5998e3bc548651cc8d4084 | C | 17,599 | 640 | /* gzlib.c contains minimal changes required to be compiled with zlibWrapper:
* - gz_statep was converted to union to work with -Wstrict-aliasing=1 */
/* gzlib.c -- zlib functions common to reading and writing gzip files
* Copyright (C) 2004-2017 Mark Adler
* For conditions of distribution and use, see http://... |
bd20fd6582621b44b6fd78f23232db7c44ea8c4f2f7a61795f05e8689607c535 | C | 17,604 | 618 | /* example.c -- usage example of the zlib compression library
*/
/*
Copyright (c) 1995-2006, 2011 Jean-loup Gailly
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 a... |
a52a5025aedbc913015901679bd6c958cce80c59bdf8501e5f92df9573e0e0fb | C | 17,987 | 687 | #include "utils.h"
#include "rld0.h"
#include "rle.h"
#include "mrope.h"
#include "htslib/kstring.h"
#include "htslib/thread_pool.h"
#include "read_thread.h"
#include "read_tags.h"
#include "ksw.h"
#include "fml.h"
#include "number.h"
#include "mag.h"
extern int ksa_sa(const unsigned char *T, int *SA, int n, int k);
e... |
8954bcbc0aec5b2d05c828b3da8f819712ff578cdafb006e4a64eebd80bbc067 | C | 18,231 | 391 | /*
* Copyright (c) 2016-present, Yann Collet, 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).
* Yo... |
f08ac45953f32f6b2cdd45bbe6be104f7b11dfaa6a5cb566ec28ebb2b7d4e075 | C | 18,239 | 629 | /* example.c contains minimal changes required to be compiled with zlibWrapper:
* - #include "zlib.h" was changed to #include "zstd_zlibwrapper.h"
* - test_flush() and test_sync() use functions not supported by zlibWrapper
therefore they are disabled while zstd compression is turned on */
/* example.c -- us... |
920599393e47b11f040e98dc64efd3c06421fbdc917e5aa706ab50788a97143e | C | 18,289 | 636 | /*
uSynergy client -- Implementation for the embedded Synergy client library
version 1.0.0, July 7th, 2012
Copyright (c) 2012 Alex Evans
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.
Per... |
7898e849f2f8da931288acfff2f74669cb04337a14bba4137e86e7b025211416 | C | 18,352 | 640 | #include "utils.h"
#include "htslib/sam.h"
#include "htslib/kstring.h"
#include "htslib/hts.h"
#include "htslib/bgzf.h"
#include "number.h"
#include <sys/stat.h>
#include "dict.h"
#include "pisa_version.h"
struct fp_out {
BGZF *barcode_fp;
BGZF *feature_fp;
BGZF *mex_fp;
};
struct files {
char *path;
... |
8f18b3c43721572a2a02578d67bc9bfb57fdd8673513c327a8b88afd17957a56 | C | 18,362 | 786 | /*
* TINYEXPR - Tiny recursive descent parser and evaluation engine in C
*
* Copyright (c) 2015, 2016 Lewis Van Winkle
*
* http://CodePlea.com
*
* 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 ... |
6e3a3b069892610b0c0dc88a7c88c3b8bbb4b82ed79257f0a9bc23c8eb1d19a2 | C | 18,424 | 423 | #include "uthash.h"
#include <stdbool.h>
typedef struct _UndirectedEdge UndirectedEdge;
typedef struct _DirectedEdge DirectedEdge;
typedef struct _Node Node;
typedef struct _NodeIndexPair NodeIndexPair;
typedef struct _LongToDirectedEdgeList LongToDirectedEdgeList;
typedef struct _ReturnElems2 ReturnElems2;
// NOTE: ... |
f9937c46184c3e2efe5746ea9501efd134b4ddc0611ce31a6c872f06f1483b68 | C | 18,429 | 692 | #include "utils.h"
#include "rld0.h"
#include "rle.h"
#include "mrope.h"
#include "htslib/kstring.h"
#include "htslib/thread_pool.h"
#include "read_thread.h"
#include "read_tags.h"
#include "ksw.h"
#include "fml.h"
#include "number.h"
#include "mag.h"
static unsigned char nt6_tab[256] = {
5, 5, 5, 5, 5, 5, 5, 5, ... |
894106f47295130015951f9e1f3a1494b1b970f2be0ff305b6adc38cfa7a8bc7 | C | 18,822 | 513 | #include "mex.h"
#include "math.h"
#include "common.c"
/*
* This function MSFM2D calculates the shortest distance from a list of
* points to all other pixels in an image, using the
*Multistencil Fast Marching Method (MSFM). This method gives more accurate
*distances by using second order derivatives and cross neig... |
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