sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8df364aecc510c0511aaf00714edc90ea026d0c96c9ca9d6cfc6cd7054f3bab6 | C | 19,184 | 645 | /* The MIT License
Copyright (c) 2008, 2012-2014, 2017 Genome Research Ltd (GRL).
2010 by 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 t... |
4d7e8ee92147c6423f6285dbc7cee768f00568603bb1c9722d1752a18fdd8f93 | C | 19,453 | 599 | /*************************************************
* 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.
... |
d8fc49a6323539f9557c2ea20b9a807bdeda6775645e3577ce7acc27d8d3c0ac | C | 19,542 | 625 | #include "utils.h"
#include "htslib/sam.h"
#include "htslib/hts.h"
#include "bam_pool.h"
#include "htslib/kstring.h"
#include "number.h"
#include "htslib/thread_pool.h"
#include "thread.h"
#include "dict.h"
#include "htslib/khash.h"
// maximal hamming distance of two similar UMI
#define UMI_E 1
extern char *compactDN... |
b3fdbc2c40264a8c2dc3aae39b351f35626ced8356ecf55e24da7480377d55de | C | 20,488 | 671 | /* gzwrite.c contains minimal changes required to be compiled with zlibWrapper:
* - gz_statep was converted to union to work with -Wstrict-aliasing=1 */
/* gzwrite.c -- zlib functions for writing gzip files
* Copyright (C) 2004-2017 Mark Adler
* For conditions of distribution and use, see http://www.zlib.net/... |
552754a0a401de18df8316558e5f942f7075e38d24493f22f6c727a72f69759a | C | 20,697 | 654 | /*
* Copyright (c) 2016-present, Przemyslaw Skibinski, 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 th... |
7436ffbdecf43e6f35500b4c32b3d4f339da7765327b03d85e445c2d254085e8 | C | 21,092 | 752 | /*
Copyright (c) 2013-2019 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,
this lis... |
23a8783e40a093a24ae5db5c0b45d42f36556eeee74e848c9801bd8b53268704 | C | 21,120 | 725 | #include <assert.h>
#include <err.h>
#include <fcntl.h>
#include <getopt.h>
#include <inttypes.h>
#include <libgen.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <strings.h>
#include <unistd.h>
#include <sys/mman.h>
#include <netinet/in.h>
#include "blast_to_fasta.h"
#include... |
8e828660bcf49cded92b3971c1a81fe5607b6bbe3632f59ec96be03e0adea2a5 | C | 21,401 | 581 | /* tabix.c -- Generic indexer for TAB-delimited genome position files.
Copyright (C) 2009-2011 Broad Institute.
Copyright (C) 2010-2012, 2014-2019 Genome Research Ltd.
Author: Heng Li <lh3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and ass... |
b55304a50d5f8aba117b3254258e0db0e17bb78188090b3ae2a8f7721ed8b546 | C | 21,481 | 733 | #include "utils.h"
#include "fastq.h"
#include "dict.h"
#include "htslib/thread_pool.h"
#include "htslib/kstring.h"
#include "number.h"
#include "read_tags.h"
#ifdef _OPENMP
#include <omp.h>
#endif
static struct args {
const char *r1_fname;
const char *r2_fname;
const char *r3_fname;
const char *r4_fna... |
5f7bdd825c9119fade692688798cf5a9a0dee15d61ed1f178301a17fd0653839 | C | 21,559 | 568 | /*************************************************
* 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.
... |
26edb58e3d1bafad3c4400debdea8236cb5903fff1084678fd10e75e1071d859 | C | 21,626 | 582 | /**
* 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"... |
0b47a51d9b905e337f6dac74e3ad75ea860713b76a08e77a1032a3bd13922f60 | C | 22,017 | 670 | /* gzread.c contains minimal changes required to be compiled with zlibWrapper:
* - gz_statep was converted to union to work with -Wstrict-aliasing=1 */
/* gzread.c -- zlib functions for reading gzip files
* Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013, 2016 Mark Adler
* For conditions of distribution and ... |
4fca506954d6a0816a957beaa6fd7873d2924378e4944d028676c9d592ac7d4f | C | 22,043 | 684 | /*
Copyright (C) 2017-2019 Genome Research Ltd.
Author: Petr Danecek <pd3@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 Software without restriction, including without ... |
46183462ee3ceb11dcf7b398a3909a2e810c2c2a19540dab7304e828cc969166 | C | 22,490 | 607 | #include "utils.h"
#include "coverage.h"
#include "bed.h"
#include "number.h"
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "htslib/kstring.h"
struct depth *depth_init()
{
struct depth *d = malloc(sizeof(*d));
memset(d, 0, sizeof(*d));
d->id = -1;
return d;
}
void depth_destroy(struct depth... |
3ad6cd72a1e0ea02d7dc0f376035f9ef87683ac769910a192b47c8dd811f7775 | C | 22,576 | 842 | /*
* 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 ... |
c60f6e11fcbfdcab286af00be90759873e964f06c62dcdf86fd9f51917233825 | C | 23,358 | 733 | #include "utils.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include "htslib/ksort.h"
#include "dict.h"
#include "gtf.h"
#include "region_index.h"
#include "number.h"
#include <zlib.h>
KSTREAM_INIT(gzFile, gzread, 8193)
KHASH_MAP_INIT_INT(attr, char*)
struct _ctg_idx {
int o... |
91312a59e6820781d4a9fcb11822e657e4e668a5aaa848167c1e22e1716fd987 | C | 23,771 | 596 | /*
* 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).
*/
... |
7d7c8fe11372781498f13141c642bb5286c05491707bf77ac57eb08362a37b98 | C | 23,855 | 499 | /*
* 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... |
368cab730937fc9608a2395c9f57f337eaaab30b27069a6e31f23f5ec477e668 | C | 24,146 | 896 | /*
hfile_s3_write.c - Code to handle mulitpart uploading to S3.
Copyright (C) 2019 Genome Research Ltd.
Author: Andrew Whitwham <aw7@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 ... |
e973c1ff769ee560f38ad0411d875c405b1dc30ba7f55b55d707e46535a25fcb | C | 24,421 | 790 | // Convert SAM records to BAM and parse barcode tag from read name to SAM attributions
#include "utils.h"
#include "number.h"
#include "htslib/thread_pool.h"
#include "htslib/hts.h"
#include "htslib/sam.h"
#include "htslib/kstring.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/bgzf.h"
#include "... |
de6f3eeddcebf45126aeaa0ca7cb87f9dbda331d02d224086433930a5c8b0150 | C | 24,613 | 618 | /*
* Copyright (c) 2015-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... |
41ea45be613a19795619741139daaab8d86af0abfa67017107540a0cab58cfc9 | C | 25,065 | 795 | /*
* FSE : Finite State Entropy encoder
* 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:
*
... |
ae247ad27842a48ac0e2dc98c633844025331dd724877c24f6e7082ef1d5a81d | C | 25,277 | 954 | /* Alternative malloc implementation for multiple threads without
lock contention based on dlmalloc. (C) 2005-2006 Niall Douglas
Boost Software License - Version 1.0 - August 17th, 2003
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying docume... |
96466f20b8e46870c05b758e873dc4ff02a69f71c1400993e63c10af805ce9f5 | C | 25,330 | 802 | #include "utils.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include "htslib/ksort.h"
#include "dict.h"
#include "gtf.h"
#include "region_index.h"
#include "number.h"
#include <zlib.h>
KSTREAM_INIT(gzFile, gzread, 8193)
KHASH_MAP_INIT_INT(attr, char*)
static char *mito = "MT";
v... |
2293d8e11bc392c44401e589b8ab246b05a6be41913ccb9e4c451c68e80b5581 | C | 25,505 | 833 | /*
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 "EM.h"
#include "gamma.h"
typedef struct args_purityEM_t{
... |
08eefa194bb505ecf645ca8e812d004bf27de9f5796a3ec518dc1963be35b426 | C | 26,069 | 924 | /* faidx.c -- FASTA and FASTQ random access.
Copyright (C) 2008, 2009, 2013-2019 Genome Research Ltd.
Portions copyright (C) 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 documentation... |
677303b4d3198c6110f18eaa2e24795926495e19877c1903e0976af5b68b3001 | C | 26,170 | 770 | /*
* Huffman encoder, part of New Generation Entropy library
* Copyright (C) 2013-2016, 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 condi... |
8c08851aad5e7db9368caec6c7907e8c56d56867d9147ff847cfd668bdecce6b | C | 26,197 | 773 | /*
* TINYEXPR - Tiny recursive descent parser and evaluation engine in C
*
* Copyright (c) 2015-2018 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 t... |
352ce6be0397d29e2ec023ee547ca0babbf0705abe035d1c16746574773c9f26 | C | 26,646 | 773 | /* Written by ruibin Xi
May 19, 2011
Modified on Feb 4 2011
* */
#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/statlib.h"
#include <getopt.h>
#include <math.h>
#define GAP_ERROR ... |
ed1e6bab7b1c3d153efa5a94191e1f797037204dde8086c2835a82709fa8aecd | C | 26,730 | 904 | /*
* Copyright (c) 2014-2019 Genome Research Ltd.
* Author(s): James Bonfield
*
* 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,
* ... |
73a909ffec7f6c5d3988b494e617bb8c4a9fd65ba24ea41af7ea60459900d0e5 | C | 26,931 | 815 | /*
* Copyright (c) 2018-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... |
daf0d99f22c51202263bda18b386d810ecebc1c4e0b24ca6140956bb38becadb | C | 27,182 | 932 | /*
* 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.c
*
* Code generation for function 'detrend'
*
*/
/* Include files */
#include "detrend.h"
#includ... |
eec3aae6858ee3b3b6f164cba9295fbced92b88f8fbf1d5dcc339b4e96a8a9ea | C | 27,322 | 728 | /*-*************************************
* Dependencies
***************************************/
#include <stdio.h> /* fprintf */
#include <stdlib.h> /* malloc, free, qsort */
#include <string.h> /* memset */
#include <time.h> /* clock */
#include "mem.h" /* read */
#include "pool.h"
#include "threading.h"
#includ... |
f199cefb3a5d46a2cd50ffd4c95ec184d672ae7427680e6e603b7145da120203 | C | 27,533 | 721 | /* ******************************************************************
FSE : Finite State Entropy encoder
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, with or without
modification, ar... |
e9536b3199b668002ff96362621c9ab19b4567573eb4aee26411d48fe6a1b31c | C | 28,209 | 809 | /*-*************************************
* Dependencies
***************************************/
#include <stdio.h> /* fprintf */
#include <stdlib.h> /* malloc, free, qsort */
#include <string.h> /* memset */
#include <time.h> /* clock */
#include "mem.h" /* read */
#include "pool.h"
#include "threading.h"
#include... |
ec4d72b4167c15f5b746bf0990349bafc1bf034ef7acffd1647666a656f730dc | C | 28,476 | 929 | #include "utils.h"
#include "json_config.h"
#include "fastq.h"
#include "kson.h"
#include "number.h"
#include "htslib/kstring.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/thread_pool.h"
#define MAX_PATTERN_LENGTH 100
#define MIN_SEED_LENGTH 6
#define MAX_SEED_LENGTH 20
#define MAX_MISMA... |
099d179b8ae850160dd3fc56c8b91be990fb3922932ab58537b8b015ab314c0e | C | 28,678 | 602 | #include "mex.h"
#include "math.h"
#include "common.c"
/*This function MSFM3D 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 ... |
6a22f0b9eda6f11f35d098b1973bab07b2cc497d144a8a361f9664e173307a3b | C | 28,942 | 876 | /*
* xxHash - 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:
*
* * Redis... |
4ecab9f18cf2cd0668a9d65a5180167b6d6b64969c669f7358768c27f76f80b1 | C | 29,236 | 938 | #include "utils.h"
#include "htslib/khash.h"
#include "htslib/kstring.h"
#include "dict.h"
#include "number.h"
#include "read_tags.h"
#include "htslib/thread_pool.h"
#include "htslib/bgzf.h"
#include <zlib.h>
#include <ctype.h>
#include <sys/stat.h>
#ifdef _OPENMP
#include <omp.h>
#endif
#define MIN_MEM_PER_THREAD 1... |
e0345b86937e48a6cc72df51eae19358ff5519e88ca8e5168dd2a19de1d43887 | C | 30,218 | 1,103 | #include "fastq.h"
#include "number.h"
#include "htslib/kseq.h"
#include "htslib/kstring.h"
#include <zlib.h>
KSEQ_INIT(gzFile, gzread)
int check_name(char *s1, char *s2)
{
int l1 = strlen(s1);
int l2 = strlen(s2);
if ( l1 != l2 ) return 1;
size_t n;
for(n = 0; n < l1; ++n, ++s1, ++s2)
if... |
66e8e6f3c8879de7c7d072d0cded9c07224b38da2410eeb6da868dc48f80f33c | C | 30,346 | 1,058 | /* Getopt for GNU.
NOTE: getopt is now part of the C library, so if you don't know what
"Keep this file name-space clean" means, talk to drepper@gnu.org
before changing it!
Copyright (C) 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995,
1996, 1997, 1998, 2005 Free Software Foundation, Inc.
NOTE:... |
989b3d29ee6e2af60ed7459390aa05c4eb9250d3a58b7534c511686a96da775d | C | 30,437 | 828 | /*
* Copyright (c) 2015-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... |
b302f8277e1fe8b2c1226e1d251d7f556ce950e437d4cbe75430246e52acbe32 | C | 31,124 | 1,146 |
#include "EM.h"
THETA new_THETA(int n_in, int EV, double an, double sx)
{ THETA theta = malloc(sizeof(struct THETA_t));
int i, n;
n = n_in;
if(n<0) {fprintf(stderr,"Error in new_THETA, n (=%d) must be nonnegative\n",n);exit(1);}
if(n<2) n = 2;
if(theta==NULL){
fprintf(stderr,"Error, memory allocation failed\n... |
6bdab3c87154c0317cf12ab566edde7d33dec51fece8bc7398a86cf2f2acf05a | C | 31,982 | 966 |
/* [ ... ] = priority( cmd , ... )
*
* Query or change the priority level of specified processes. cmd is a
* single char used to select the form and action of the function:
*
* [ pid , exe ] = priority( 'i' , names )
*
* Find processes that have executables listed in names, a cell array
* o... |
5c41c7e6fd0cf01b94a6287ce64f63fe0b962bea2348566537acc4c3eb23198a | C | 32,244 | 1,181 | /**
* 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"... |
c67f657c345a152ad24d4eda0482757cce10ca6850cdf764f75780b04b46fd50 | C | 32,697 | 797 | /* ******************************************************************
Huffman encoder, part of New Generation Entropy library
Copyright (C) 2013-2016, 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
... |
034d05ff23f4ad14f1a5afe311536283b50700588c252f74694423f8baad0254 | C | 33,126 | 960 | /*
* Huffman decoder, part of New Generation Entropy library
* Copyright (C) 2013-2016, 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 condi... |
4cf57d29a0ec3be8f094a366292abf988082668317aff94d41405dcc062fceac | C | 33,201 | 951 | /* Written by ruibin Xi
May 19, 2011
* */
#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/statlib.h"
#include <getopt.h>
#include <math.h>
#define GAP_ERROR 2
static int no_header=0;... |
0ccdfcaf2ab0475a35455b8152a4bbc987f542ec085e12f4ab616a6f402595f2 | C | 33,375 | 1,197 | #ifdef _OPENMP
#include <omp.h>
#endif
#include<R.h>
#include<Rdefines.h>
#include <assert.h>
#include "perm.h"
#include "sparse_ops.h"
#ifndef Matrix_stubs
#define Matrix_stubs
#include "Matrix_stubs.c"
#endif
#define CACHE_PER_BATCH 10000
#define MIN_HIT 1
SEXP openmp_support()
{
#ifdef _OPENMP
return Scalar... |
e476562165dd063f9ab09b3bb12b996ce18cb2a16e58682046cf82bb2c1772dd | C | 33,404 | 831 | /* vcfutils.c -- allele-related utility functions.
Copyright (C) 2012-2018 Genome Research Ltd.
Author: Petr Danecek <pd3@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 Software w... |
b8b68d3cb01e55868674357976441b0aa9b42a1f0eec6cb559ea1215727576fe | C | 33,428 | 1,153 | /* hfile.c -- buffered low-level input/output streams.
Copyright (C) 2013-2019 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 Soft... |
8c951b5bed259df1f53c63d464218626a8d689310b2f3fdd626391cc321bd2c5 | C | 34,831 | 1,257 | /* hfile_s3.c -- Amazon S3 backend for low-level file streams.
Copyright (C) 2015-2017, 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 de... |
b83999f35da38ea28ced7a8287d0b9069a51df2fea6eddf3b911beeaa3dd8d4b | C | 35,071 | 887 | /*
* 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... |
52d2e5c6d3620a1ae34ef1b4315fd98072086de042a9986bbe1891058c20011a | C | 35,280 | 1,162 | /*
Parse and trim single cell LFR adaptors and barcodes
demo:
{
"pattern":"CCCCAGAACGACATGGCTACGAAGTCGGANNNNNNNNNNNNNNNNNNNCCTTATCAGCGTCCGACTTCGTAGCCATGTCGTTCTGCG(T1)CCTTCC(T2)CGATG(UM)[polyT]",
"segments":[
{ // LFR cell barcode
"tag":"CB",
"seg":[ // two segments
... |
e035f3a78f3de9be304b41f462786c9f444476ecacd2e58b8c2f985b0f033358 | C | 35,347 | 1,153 | //
#include "utils.h"
#include "dict.h"
#include "region_index.h"
#include "htslib/kstring.h"
#include "htslib/kseq.h"
#include "htslib/vcf.h"
#include "bed.h"
#include "number.h"
#include <zlib.h>
KSTREAM_INIT(gzFile, gzread, 8193)
static const char *bed_anno_type[] = {
"unknown",
"promoter", // use for old ... |
0c3b43f17936d452deb64d54d9f5ddec0f4b03e30738cddf95ad5af1a32484c9 | C | 35,474 | 552 | #include <stdio.h>
int frag_count_usage()
{
fprintf(stderr, "# Generate peak-by-cell fragment count matrix.\n");
fprintf(stderr, "\n");
fprintf(stderr, "\x1b[36m\x1b[1m$\x1b[0m \x1b[1mPISA\x1b[0m count2 -bed peaks.bed -t 10 -list barcodes.txt -outdir exp fragments.tsv.gz\n");
fprintf(stderr, "\nOptions... |
300f878ba86026d21c63b42f8a78ca097f071a5c6087cabfe60226f8b0bea17a | C | 36,168 | 1,081 | /*
* 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... |
5b92e7034ea91af200588a29d55bfc7b512637be7fdc2bbba62b8f354d81bb9b | C | 36,403 | 1,172 | //
#include "utils.h"
#include "dict.h"
#include "region_index.h"
#include "htslib/kstring.h"
#include "htslib/kseq.h"
#include "htslib/vcf.h"
#include "bed.h"
#include "number.h"
#include <zlib.h>
KSTREAM_INIT(gzFile, gzread, 8193)
static const char *bed_anno_type[] = {
"unknown",
"promoter", // use for old ... |
960b1e42f9a43d79da2ef36a7d40d5a9214845a2028454639ef7332d9bb1c02c | C | 38,083 | 1,068 | #include <R.h>
#include <Rdefines.h>
#include <Rinternals.h>
#include "utils.h"
#include "dict.h"
#include "gtf.h"
#include "bed.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"
#define UP... |
c5c9c0a4a01012462a254672b8b56097859d7f22d786f016a4528c5e5063a690 | C | 39,480 | 1,222 | // count reads/fragments matrix for single-cell datasets
#include "utils.h"
#include "number.h"
#include "dict.h"
#include "dna_pool.h"
#include "htslib/khash.h"
#include "htslib/kstring.h"
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "htslib/thread_pool.h"
#include "htslib/hts_endian.h"
#include "pisa_ver... |
c6f4aa825f93cfdffa26db138249be98bc2e98060425d374888b8af36d4ee510 | C | 40,146 | 1,105 | /*
* Copyright (c) 2016-present, Przemyslaw Skibinski, 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 th... |
5089ceb6b30c91ce44c7c3e7392806c1be241af89dea7508e243a7b7be73131a | C | 40,360 | 1,285 | /* synced_bcf_reader.c -- stream through multiple VCF files.
Copyright (C) 2012-2019 Genome Research Ltd.
Author: Petr Danecek <pd3@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 ... |
1bc64f6bab0762547203036c80e8421a58af79d6209d0192ea84554c70a6292d | C | 40,771 | 1,159 | // parse barcode sequence from reads, rename read name with barcode tags
#include "utils.h"
#include "json_config.h"
#include "ksort.h"
#include "fastq.h"
#include "kson.h"
#include "number.h"
#include "htslib/kstring.h"
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "sim_search.h"
#ifdef _OPENMP
#include... |
4637bcdf78e46a77e0ca0f30346acd3d41fed3d6fe7947c857abfc61276abeee | C | 42,295 | 1,128 | /*
* 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... |
efc4752e30ba77ace05b24338a5320ef6a996ecda394208727f9e53af900ed70 | C | 42,381 | 1,432 | /* thread_pool.c -- A pool of generic worker threads
Copyright (c) 2013-2019 Genome Research Ltd.
Author: James Bonfield <jkb@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 Softwa... |
f66ba2613efe20269a79f7562d24f99d2f04bc20a44b8f93e7f10bc42c2a7b4b | C | 42,576 | 1,527 | /*************************************************
* 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.
... |
11ef0a5b4d5652f2f58d3941bce3cabf3f9ef8022033d8c41bfd68b7069de231 | C | 43,684 | 1,111 | /*
* 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... |
69bde60d3da73355cf1940fc561174bb399bee4a4fe34b4297d7fdf902069861 | C | 45,479 | 1,015 | /*
* Copyright (c) 2016-present, Przemyslaw Skibinski, 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 th... |
b9451cac7842ae9eb7a92698594c5ff37295903b388f0f8b36ab2f5c69fffd9e | C | 45,796 | 1,096 | /* ******************************************************************
huff0 huffman decoder,
part of Finite State Entropy library
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, with or... |
a9e95f29c43d607996f6f22e874a9b164d077c43b0de803d4ef8195c522f9204 | C | 46,432 | 1,009 | /***************************************************************************\
|* *|
|* Copyright NVIDIA Corporation. All rights reserved. *|
|* *|
|*... |
1ec7966c5f141358043b0cf0ec62c4e9af521a1633f9c30a1a30219a7a361b63 | C | 46,930 | 1,504 | /* hfile_libcurl.c -- libcurl backend for low-level file streams.
Copyright (C) 2015-2017, 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... |
0f1ab290702ce31dac7b3bafc04388c5feff0f8aa587536aecdf9be0d5a81bb5 | C | 48,900 | 1,594 | /*
* 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 ... |
82d8229b523fd9a56ae3daa638245b493cef433cf5498dcd48d64747bd6eea3d | C | 50,874 | 1,106 | /*
* 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... |
dd5ed0ccf7cdea55adb377acccbf0db24b6bac762f299cf55b41e0c6052ec52c | C | 51,479 | 1,098 | /*
* 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... |
72f6d3905e33968e9bf1d388088c08f2a2cf0661c79ded937cc75adeef9b6b71 | C | 52,895 | 1,136 | /*
* Copyright (c) 2016-present, Przemyslaw Skibinski, 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 th... |
7697c85b835117b9b4a483155ac88f45ffad8de3e9653fde7a5781b0a8a59d9f | C | 54,005 | 1,239 | /*
* 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... |
59dcbff10aa7f9a9e5374d9ab45199f3c5c90221648418ef1a4253e5327a273d | C | 54,649 | 1,913 | /*
* divsufsort.c for libdivsufsort-lite
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* 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 wit... |
6d4e84fc8af84927dd84b1b5e9a5a3f9779f0f50990ece88d3a5752c740de9fe | C | 60,155 | 1,789 | // annotate Gene or Peak to SAM attribution
#include "utils.h"
#include "number.h"
#include "htslib/khash.h"
#include "htslib/kstring.h"
#include "htslib/sam.h"
#include "htslib/khash_str2int.h"
#include "htslib/kseq.h"
#include "htslib/hts.h"
#include "htslib/bgzf.h"
#include "bam_pool.h"
#include "htslib/thread_pool.... |
461d7bf74c08dd0cfe8569ea54fdfc045196775157e6b84252b0eb50fc8998ca | C | 64,385 | 2,254 | /*
Copyright (c) 2012-2019 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,
this lis... |
14d2a0ff25b95e94e7af29672a434d60c173ce855622a1b2ce4506e2fee2a736 | C | 66,411 | 1,607 | /*
* 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... |
69a4b44687dcd5d1fd35adfee270fdbc0bfd836a277a114f1a2343bb902452a6 | C | 69,329 | 1,928 | /*
* Copyright (c) 2017-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... |
6e58762dc4c720fc34b6b3ce19fddd80a40d64b32c6fdd838adf0e959d235da0 | C | 70,527 | 2,133 | /*
* 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... |
8e40592770bfa8fabb52ab5fd24e7bb1617f2e592ee05198b57e8dad1288937d | C | 75,749 | 2,420 | /* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
2011, 2012 Attractive Chaos <attractor@live.co.uk>
Copyright (C) 2009, 2013-2019 Genome Research Ltd
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software ... |
6a8e95a887aa0da9ca10849f647ca1874599ada327c1558576f63c5769e5a80d | C | 79,034 | 2,711 | /*
Copyright (c) 2018-2019 Genome Research Ltd.
Authors: James Bonfield <jkb@sanger.ac.uk>, Valeriu Ohan <vo2@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... |
9283deffef530c38deabfe919ffb13c740caf660261de773f12de988bd1be3d2 | C | 79,831 | 2,858 | /*
* 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 ... |
40099982889b783f1f2f7ad4297e0a7a85387e3835d8d5d6d97f1e2e724b512a | C | 82,225 | 2,526 | /**
* Copyright (c) 2016-present, Yann Collet, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under the BSD-style license found in the
* LICENSE file in the root directory of https://github.com/facebook/zstd.
*
* This program is free software; you can redistribute it and/or modify it unde... |
8faee3a1fe90173dff2d6ee94c2c0a846c98de0ee97de1372a8ce8735a067698 | C | 83,491 | 1,344 | #include <GL/gl3w.h>
#ifdef _MSC_VER
#pragma warning (disable: 4055) // warning C4055: 'type cast' : from data pointer 'void *' to function pointer
#pragma warning (disable: 4152) // warning C4152: nonstandard extension, function/data pointer conversion in expression
#endif
#ifdef _WIN32
#define WIN32_LEAN_AND_MEAN 1... |
8addbec02565d284f394189b9491b1b609d87d0ece5489e54d705c55854f952d | C | 85,784 | 3,016 | /**
* 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"... |
eafc799c3117da9db5ac056849e1fec43ce54d55575c64756dba5c4a140293f3 | C | 90,084 | 2,303 | /*
* 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).
*/
/// Zstandard... |
77f31adfadf4c6340502f4d260492af7c3e9caad3994408e03342bfcc28e7199 | C | 90,245 | 2,046 | /*
* 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... |
04fcc3016ac1ad0a034ae8d6dbef8c95bd3236457e7303f4d951b0c0f4389101 | C | 93,799 | 2,516 | /*
* 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.c
*
* Code generation for function 'multitaper_spectrogram_coder'
*
*/
/* Inc... |
e75947c64ad72f8631479984e4b7c36df8a1bc8f3f285a06e0a720183637f304 | C | 94,781 | 2,363 | /*
* 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... |
d1cb62f05ecd005e30f22b11ece6f217e6b85d048254fdac84bccc6f8b98f000 | C | 100,463 | 2,783 | /*
* Copyright (c) 2015-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... |
2ed1c811996abd81427d345606263305d547c4b1699b67a1fe2ffd4dd0f47b2e | C | 101,700 | 2,146 | /*
* Copyright (c) 2015-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... |
4cacbd3797895cdd14a0847b6c755fd71dee25178bab270e939ff64fb7256f6e | C | 108,991 | 2,257 | /*
* 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... |
fe0ba5667d83aed9c2037612188ca8e56bf5920a997a68dc9532de0dfde3a5c7 | C | 113,417 | 3,130 | /*
* 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... |
e68b17f71a39d5cf098ab9dea6ba050582629832e0d657dff3fef99c5372bc8e | C | 115,996 | 3,375 | /*
Copyright (c) 2012-2019 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,
this lis... |
e02ec1cb81210165607e3f540a552986f33176fceb0d27e06cd5fe9a8a571b54 | C | 119,220 | 3,431 | /*
Copyright (c) 2012-2019 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,
this lis... |
5bc95328c9b7806f851de605a8e516f1b7c575f6e6a13ae20c13c83b28228c4f | C | 121,941 | 3,493 | /*************************************************
* 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 (but see
below fo... |
0b3e5197759a43b5e9c8da02c0984498071a08ba3ece123165d556de27286e88 | C | 123,556 | 3,903 | /* hts.c -- format-neutral I/O, indexing, and iterator API functions.
Copyright (C) 2008, 2009, 2012-2019 Genome Research Ltd.
Copyright (C) 2012, 2013 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 as... |
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