sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d8990168bff3e3e8271c9d90f9e27862a2b1038b583976604361059acc89d6c6 | C | 5,130 | 154 | /* dict.c -- create a sequence dictionary file.
Copyright (C) 2015 Genome Research Ltd.
Author: Shane McCarthy <sm15@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 withou... |
31e9b50fcab31fa13ef904caf817b8ed7ec0cd7c95021c63cbeb72748296edbb | C | 5,174 | 184 | // interp4_table_mex.c
// Mex file for 4D periodic interpolation using tabulated interpolator.
// see interp4_table1_for.c
// Copyright 2004-03-30 Yingying Zhang and Jeff Fessler, University of Michigan
// Extended 2013-08-02 to 4D by David Johnson, The Ohio State University Wexner Medical Center
#include "def,table.h... |
f622a537d0d127076c2b94955f3bad7281f3433a5902f06b38b269d639158687 | C | 5,216 | 194 | /* test/split/test_filter_header_rg.c -- split test cases.
Copyright (C) 2014 Genome Research Ltd.
Author: Martin O. Pollard <mp15@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 S... |
eeb1e92dc22c5aff0aa93193ac453d7980eed47bc94398ac13f6fd60fa5c8cb8 | C | 5,373 | 183 | // interp4_table_adj_mex.c
// see interp4_table1_adj.c
// Mex file for *adjoint* of 2D periodic interpolation using table lookup.
// ck = interp4_table_adj_mex(fm, h1_table, h2_table J, L, tm, K)
//
// Copyright 2004-4-2 Jeff Fessler and Yingying Zhang, University of Michigan
// Extended 2013-08-02 to 4D by David Johns... |
2115cb42a170c57b600eebaab66d9a99fca2cd27ade69f14e5184988fff8438d | C | 5,434 | 159 | #include <TH/TH.h>
#include "batchnormp.h"
#define THNN_CHECK_SHAPE(I1, I2) \
if (I1 != NULL && I2 != NULL && !THFloatTensor_isSameSizeAs(I1, I2)) \
{ \
THDescBuff s1 = THFloatTensor_sizeDesc(I1); \
THDescBuff s2 = THFloatTensor_sizeDesc(I2); \
THError(#I1 " and " #I2 " shapes do n... |
0b9d186c8b887b48fabccb1d184a261d9cd543e5f52af1ef75063cd34c9a52ef | C | 5,458 | 177 | /* sample.c -- group data by sample.
Copyright (C) 2010, 2011 Broad Institute.
Copyright (C) 2013, 2026 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 associated documentation files (the "Software"... |
c0423c068d0ee4ea9409a66984535a487ed4f1f14b46a142523ffaac3ba8b31a | C | 5,711 | 155 | /* sam_opts.c -- utilities to aid parsing common command line options.
Copyright (C) 2015 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
... |
f83f96da7c58eb7142a2c61cfb633d900596fa32d562696cf48bf2b2fd57a8dc | C | 5,714 | 220 | /*
* R : A Computer Language for Statistical Data Analysis
* Copyright (C) 1999-2014 The R Core Team
*
* 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... |
ac04289ebfaf2cae754fd9db86fcf491a9deef48f02ae2bc60c7bfa433396206 | C | 5,843 | 213 | //####################################################################
//ICA test
//####################################################################
//2 May 2004
//Contact: kraskov@its.caltech.edu
//####################################################################
//uses mic_xnyn, mir_xnyn
#include <stdio.h>
#i... |
2a4f55530f15b89342de635b61bc31d1b7cd757295272997368790f42071d55b | C | 5,860 | 193 | /* sam_utils.c -- various utilities internal to samtools.
Copyright (C) 2014-2016, 2018, 2019, 2023 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")... |
3d1162ae43765f291770903289f270d3aeb5d811bc0ada65a289dc4edce62230 | C | 5,878 | 373 | //
// testmpl.c
// MorPhy2
//
// Created by mbrazeau on 12/05/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#include "mpltest.h"
#include "testmpl.h"
int test_create_destroy_Morphy(void)
{
theader("Test simple create/destroy");
int failn = 0;
Morphy new = mpl_new_Morphy();
if ... |
4e343af50229234e1949404b09541cbf9a9015706acffc0bab50c1ae89670a00 | C | 5,912 | 179 | /* bedcov.c -- bedcov subcommand.
Copyright (C) 2012 Broad Institute.
Copyright (C) 2013-2014 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 associated documentation files (the "Software"), to deal... |
f9962a89d70d1aa7c33512c5dcd3f3f77347d8979776c82a630416492b2b4a05 | C | 5,998 | 174 | /* test/split/test_expand_format_string.c -- split format string test cases.
Copyright (C) 2014-2015,2024 Genome Research Ltd.
Author: Martin O. Pollard <mp15@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "... |
8321048a80b447e7f6ddbe336302162e4fdea349e6bf3aa2f75b7f1c6b3de37f | C | 6,335 | 163 | #include "../headers/topology.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software")... |
af3da270853c4c1e0ab72944861b45c814e95a8a86248b0cc7d027a9501102a2 | C | 6,352 | 252 | #include <R.h>
#include <Rinternals.h>
#include "mpl.h"
#include "RMorphyUtils.h"
SEXP _R_wrap_mpl_new_Morphy(void)
{
Morphy new = mpl_new_Morphy();
SEXP result = R_MakeExternalPtr(new, R_NilValue, R_NilValue);
return result;
}
SEXP _R_wrap_mpl_delete_Morphy(SEXP MorphyHandl)
{
int ret = 0;
S... |
94c8f2c63bbf8a0bf4beb5c1620c48115321dddffc33dcc65a892cbd781650cd | C | 6,362 | 252 | #include <R.h>
#include <Rinternals.h>
#include "../../src/mpl.h"
#include "RMorphyUtils.h"
SEXP _R_wrap_mpl_new_Morphy(void)
{
Morphy new = mpl_new_Morphy();
SEXP result = R_MakeExternalPtr(new, R_NilValue, R_NilValue);
return result;
}
SEXP _R_wrap_mpl_delete_Morphy(SEXP MorphyHandl)
{
int ret ... |
af91b9e1d9ec719f05133324282cdc77bc2f6245fca5034b8d0962bdec61369e | C | 6,405 | 245 | /*<html><pre> -<a href="index.htm#TOC"
>-------------------------------</a><a name="TOP">-</a>
random.c and utilities
Park & Miller's minimimal standard random number generator
argc/argv conversion
Used by rbox. Do not use 'qh'
*/
#include "libqhull.h"
#include "ran... |
f81f946fd08ddd8caad8a32c2282c7df8fd376712249a6fc2b7da076eebd66ec | C | 6,405 | 198 | /* test/test_view.c -- simple view tool, purely for use in a test harness.
Copyright (C) 2012 Broad Institute.
Copyright (C) 2013-2014 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 associated docu... |
fd0bf6edb67c2d8a37e8aebba19a91f2a1ae9105833e80be0704dfd719300979 | C | 6,468 | 247 | /*<html><pre> -<a href="index_r.htm#TOC"
>-------------------------------</a><a name="TOP">-</a>
random_r.c and utilities
Park & Miller's minimimal standard random number generator
argc/argv conversion
Used by rbox. Do not use 'qh'
*/
#include "libqhull_r.h"
#includ... |
4e827dfe80a2722d0d0b622fb1a16e13ff8a88e3bc7871b86cdf111dcae60e88 | C | 6,484 | 199 | /* maq2sam.c -- convert MAQ output to SAM.
Copyright (C) 2008, 2009 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 associated documentation files (the "Software"), to deal
in the Software without restr... |
c2e0c380a4257b7fa13c6f0462f28ae3c81a39c91a484be221333db215f053ba | C | 6,495 | 194 | /* errmod.c -- revised MAQ error model.
Copyright (C) 2010 Broad Institute.
Copyright (C) 2012, 2013 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 associated documentation files (the "Software"), ... |
e13077776b12472574981c6b56aa30ab4b124903b8f0c459273ada3e5f15e17c | C | 6,547 | 403 | #include <stdio.h>
#include "mpltest.h"
#include "../src/statedata.h"
int test_get_states(void)
{
theader("State-extraction and conversion");
int failn = 0;
char *rawmatrix = "001101--- -100? ?[xyz876jkjk]ABaC434(59)9???";
// char *states = "01ABaC4359";
char *retstats;
Morphy m1 = mpl_ne... |
8f13ab5acf15c046a43e269de1c54d5fc048d4545befeb732b5a7586a707a63e | C | 6,580 | 277 |
#include "../headers/voronoi_lst.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Softwa... |
091bc7b0831748fd9a7dbe535f2d7f74a9a01a5c93001b6886c565286d1d8fae | C | 6,622 | 287 | // interp2_table1_for.c
// 2D periodic interpolation using table lookup.
//
// forward direction: (for m = 1,...,M)
// f(t_m) = \double_sum_{k1,2=0}^{K1,2-1} c[k1,k2]
// h_1( (t_m1 - k1) mod K1 ) h_2( (t_m2 - k2) mod K2 )
//
// adjoint direction: (for k1,2=0,...,K1,2-1) (note complex conjugate!)
// c[k1,k2] = \sum_{m=1... |
1f924345c1ae15ca8dfad3a7cdcb5f7e68250f69f9685293f1120b115447853d | C | 6,700 | 275 | // interp2_table1_adj.c
// *adjoint* of 2D periodic interpolation using table lookup.
//
// forward direction: (for m = 1,...,M)
// f(t_m) = \double_sum_{k1,2=0}^{K1,2-1} c[k1,k2]
// h_1( (t_m1 - k1) mod K1 ) h_2( (t_m2 - k2) mod K2 )
//
// adjoint direction: (for k1,2=0,...,K1,2-1) (note complex conjugate!)
// c[k1,k2... |
8c773407d39c04bd8906885bc4dc6511016713e1179212b315f652ad76f48170 | C | 6,729 | 202 | /*
* R : A Computer Language for Statistical Data Analysis
* Copyright (C) 1999-2016 The R Core Team
*
* 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... |
64e99afd164460656792ab69723e8df425f401c51b27dc6f572f10e42eea7fff | C | 6,730 | 241 | #include "../headers/refine.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), ... |
f0454eae7a1bed3c628b9519b94b40c5a62f4d7c0bb9bc8cb780f318001d3419 | C | 6,748 | 217 | /* test/split/test_parse_args.c -- split test cases.
Copyright (C) 2014-2015 Genome Research Ltd.
Author: Martin O. Pollard <mp15@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 So... |
978be382734656fb13b0f980deddb75174c267a4ad8ab53317b9bf3c49d7e4ab | C | 6,762 | 195 | #include "../headers/mdpout.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), ... |
fb4df7c5e5e179af73894cacbe2128040ac5fee7da2d7590dc8200e69459bef3 | C | 6,809 | 234 | /* htsfile.c -- file identifier and minimal viewer.
Copyright (C) 2014-2016 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... |
8856eb7be5bf4e1ff796b6bb7b02de5458166534892ef095cb047e0adc723ee1 | C | 6,823 | 217 | /* test/split/test_parse_args.c -- split test cases.
Copyright (C) 2014 Genome Research Ltd.
Author: Martin O. Pollard <mp15@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... |
f6e5a7afa11923b01c5e65bb22066e883946a823ea0798ee6643870648e3553f | C | 6,852 | 206 | /* test/hfile.c -- Test cases for low-level input/output streams.
Copyright (C) 2013-2014 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
... |
6fea0e622ff7757569df705d57443b2cb4c3bbf64b4391d41f8e1108bdf683a4 | C | 6,949 | 225 | /* bam_lpileup.c -- lplbuf routines.
Copyright (C) 2008, 2009, 2013 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 associated documentation files (the "Software"), to deal
in the Software without restr... |
cbc62c231b53e378908daf45b27071e9f3b0fca9f1ef4ffcac04c205d9705628 | C | 6,950 | 225 | /* bam_lpileup.c -- lplbuf routines.
Copyright (C) 2008, 2009, 2013 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 associated documentation files (the "Software"), to deal
in the Software without restr... |
cda8463b5ef6a097b52670cd88f1df00609fd772fd5fe2b3146a9575289d9e2f | C | 6,960 | 286 | #include <stddef.h>
#include <stdlib.h>
#include <math.h>
#include "phil.h"
#include "svdcmp.h"
/************************************************************************/
static double pythag (double a,
double b);
/************************************************************************/
stat... |
414b612e7a2b6205709f602c9d3157b483a4eaa9061b01feaabd58dd8bb0d700 | C | 7,131 | 236 | #include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <getopt.h>
#include <inttypes.h>
#include "htslib/faidx.h"
#include "htslib/kseq.h"
void print_version(void);
int fgets2(FILE*f, unsigned char *s, int l) {
return (fgets((char*) s, l, f))?strlen((char*)s):0;
}
KSTREAM_INIT(FILE*, fgets2, 65536)
... |
37b98e6770fffdc9f42687f57d138da60df2a1dbc52bac7d82681c8078598797 | C | 7,278 | 276 | /* The MIT License
Copyright (C) 2011 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 the Software without restriction, including
without limitation t... |
ca05409bc46bee5e10b45d9637f3fa883c28851f858eb7abd163bbdef60f222c | C | 7,293 | 227 | /* bam_rmdupse.c -- duplicate read detection for unpaired reads.
Copyright (C) 2009, 2015 Genome Research Ltd.
Portions copyright (C) 2009 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 docu... |
de9a9729537798b9bcdbd39196df4643096adf7b6492df6ec1b299068e4118b1 | C | 7,332 | 320 | #include <math.h>
#include "mex.h"
/* Input Arguments */
#define V0 prhs[0]
#define MSP prhs[1]
#define M1 prhs[2]
#define M2 prhs[3]
#define MR prhs[4]
#define E2X prhs[5]
#define E2Y prhs[6]
#define E3 prhs[7]
#define OMLEN prhs[8]
/* Output Arguments */
#define FK plhs[0]
#define P... |
cdd380520d1b131df96e000eed19d2bfa40571d5751f70e8b2c0b9facea11bec | C | 7,400 | 179 | /* bam_stat.c -- flagstat subcommand.
Copyright (C) 2009, 2011, 2013-2015 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 associated documentation files (the "Software"), to deal
in the Software without... |
95090c38c9b0c3b2aee14535e99287f50b166115031043f910f10cd34011d8bd | C | 7,440 | 215 | /* test/sam.c -- SAM/BAM/CRAM API test cases.
Copyright (C) 2014-2015 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 Software with... |
4025fd8c20a979971d326f3c4015a05a5255766ea69e21b624f9c33c6609860a | C | 7,608 | 221 | /* stats_isize.c -- generalised insert size calculation for samtools stats.
Copyright (C) 2014 Genome Research Ltd.
Author: Nicholas Clarke <nc6@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... |
c2e1fb42c29842b8585615f10739152c98c292317b64079aa005af932b4edc52 | C | 7,856 | 244 | /* bam_rmdupse.c -- duplicate read detection for unpaired reads.
Copyright (C) 2009, 2015, 2016, 2019, 2026 Genome Research Ltd.
Portions copyright (C) 2009 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 a... |
ad2da097ec998c2fe2f5d7c48e599729e66ac4f12fc9953c3a3ccd027450a4b6 | C | 7,872 | 336 |
#include "../headers/sort.h"
/*
## GENERAL INFORMATION
##
## FILE sort.c
## AUTHORS P. Schmidtke and V. Le Guilloux
## LAST MODIFIED 28-11-08
##
## SPECIFICATIONS
##
## This file contains routines used to sort atoms and vertices systems using
## coordinates x, y or z. We define a structure containing al... |
5e1a360545aecec45eee2f4b4136efb4b5a1e8414154768e398ab00a5971ed30 | C | 7,892 | 312 | #include <math.h>
#include "mex.h"
/* Input Arguments */
#define FMINTAU prhs[0]
#define MSP prhs[1]
#define M1 prhs[2]
#define M2 prhs[3]
#define MR prhs[4]
#define E2X prhs[5]
#define E2Y prhs[6]
#define E3 prhs[7]
#define OMLEN prhs[8]
/* Output Arguments */
#define FJ plhs[0]
#def... |
c999619c21e15cc4c5ce3f473a0e3f7151134850491d1ba4c5ac8a1eb73acd79 | C | 7,892 | 225 |
#include "../headers/fpocket.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software")... |
3c0a458c8e8683020a5f12411abdbae6b10ee6e64e9b6531dad0f5f2275a23ee | C | 7,917 | 272 | //
// testtreeopt.c
// morphylib
//
// Created by mbrazeau on 09/07/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#include "mpltest.h"
#include "../src/morphydefs.h"
int test_do_fullpass_on_tree(TLtree* t, Morphy m)
{
int length = 0;
int i = 0;
int end = 0;
int index = 0... |
9befc85e3ec649d8aebc9f5273d1b46e5f69e6cd9057b95b4a93ea1def00d8f7 | C | 7,918 | 274 | //####################################################################
//Mutual Information Clustering, rectangular version
//####################################################################
//2 May 2004
//Contact: kraskov@its.caltech.edu
//####################################################################
//use... |
e80fbbf66cf973aac9475f70dd92693e72f57856d58128163697bdc6abc05ac3 | C | 7,943 | 278 |
#include "../headers/psorting.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"... |
2045437e3303b917f8965bac5f020b3d1e511c580a7d6ddb4fa7d2db4f32795f | C | 7,972 | 337 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mech_api.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if ... |
8583e0100b9cbcd0a334b466a16c9aea64fd82c1d8813b5d04236734322bf4ec | C | 8,133 | 380 | #include "tldefs.h"
#include "treelib.h"
#include "tltree.h"
#include "tlnewick.h"
#include "tlutils.h"
#include "tlerror.h"
//#include <stdio.h>
TLP tl_TLhandle2TLP(TLhandlp TLhandle)
{
return (TLP)TLhandle;
}
TLhandlp tl_TLP2TLhandle(TLP tlp)
{
return (TLhandlp)tlp;
}
TLtree *tl_createtree(const int nta... |
7fe3200b42529a5817c95bd3c4ca7ac3e60e339b3c67f821db11bd9450060a04 | C | 8,148 | 238 |
#include "../headers/writepdb.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software... |
eaf2e38a69780fe5e42bce6c6b3a494068aa985300444f182fc329384c26c217 | C | 8,220 | 243 | /* stats_isize.c -- generalised insert size calculation for samtools stats.
Copyright (C) 2014, 2018 Genome Research Ltd.
Author: Nicholas Clarke <nc6@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... |
b096a2c3cc7777bb36db4c71f8fff348b6e1e4e75b028d81d2159f1a0fafef3d | C | 8,523 | 244 | /* cut_target.c -- targetcut subcommand.
Copyright (C) 2011 Broad Institute.
Copyright (C) 2012-2013, 2015 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 associated documentation files (the "Softwa... |
0ed30d9c6e1ac911a758bdab4da8cf97b4f02fff1b4770f694e327ddcfb076b3 | C | 8,605 | 272 | /* dict.c -- create a sequence dictionary file.
Copyright (C) 2015, 2020, 2026 Genome Research Ltd.
Author: Shane McCarthy <sm15@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 Sof... |
9da8d246a30454f56cae86c2f484f6d87025275a33bd08a150294f306e52f716 | C | 8,696 | 260 | /* bedidx.c -- BED file indexing.
Copyright (C) 2011 Broad Institute.
Copyright (C) 2014 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 associated documentation files (the "Software"), to deal
in t... |
5b5922a98c5e61bb5b110d8d85453afffc0d4c2dcbff7372387a5aff7f4ed585 | C | 8,712 | 242 | #include "MethylDackel.h"
#include <ctype.h>
#include <limits.h>
#include "htslib/kseq.h"
#include <assert.h>
KSTREAM_INIT(gzFile, gzread, 8192)
//returns <0 if region0 comes before region1
//returns >0 if region0 comes after region1
//returns 0 on overlap
static inline int64_t compareRegions(int32_t tid0, int32_t sta... |
1c48b74f73ccc884e5dd8c37e968f599a5e54960c6d42a134b79ec0c2270bb65 | C | 8,782 | 248 |
#include "interp_field.h"
#include <string.h>
#include <math.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_math.h>
/*
* Linear interpolation of a vector field
* Input position is in Cartesian coordinates (um)
* Output vector is normalized
* NOTE: we check if position is in bounds
*/
#define C(j,i,k) ((size_t... |
b0fa69890f57b0067d2c08de0458d01acff2d49048954609d48e50534edb3a48 | C | 8,829 | 247 | /* bam.c -- BAM format.
Copyright (C) 2008-2013, 2015 Genome Research Ltd.
Portions copyright (C) 2009-2012 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 files (the "Software"... |
c637bb8caae2ff5e167a9218ee16fa61feed6fb553254a53ee43ce7572422722 | C | 8,855 | 358 | // interp3_table1_adj.c
// 3D periodic interpolation using table lookup: adjoint.
//
// forward direction: (for m = 1,...,M)
// f(t_m) = \double_sum_{k1,2,3=0}^{K1,2,3-1} c[k1,k2,k3]
// h_1( (t_m1 - k1) mod K1 ) h_2( (t_m2 - k2) mod K2 ) h_3( (t_m3 - k3) mod K3 )
//
// adjoint direction: (for k1,2,3=0,...,K1,2,3-1) (no... |
013f96df76ce141c9e553d2b178c853b244cb9d6463471e1b2e5147aac893300 | C | 8,962 | 381 | // interp3_table1_for.c
// 3D periodic interpolation using table lookup.
//
// forward direction: (for m = 1,...,M)
// f(t_m) = \double_sum_{k1,2,3=0}^{K1,2,3-1} c[k1,k2,k3]
// h_1( (t_m1 - k1) mod K1 ) h_2( (t_m2 - k2) mod K2 ) h_3( (t_m3 - k3) mod K3 )
//
// adjoint direction: (for k1,2,3=0,...,K1,2,3-1) (note comple... |
86a0cd0dfe95ffe9553f38a2b1cd5c853aa1a645b0acfd81a59003b26a007fef | C | 9,010 | 296 | /* bamshuf.c -- collate subcommand.
Copyright (C) 2012 Broad Institute.
Copyright (C) 2013, 2015 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 associated documentation files (the "Software"), to d... |
957be1759833100f0a006b0a4aac335890b0115b223fc875dd1a5a9bfd38b0e4 | C | 9,028 | 275 | #include <stddef.h>
#include <stdlib.h>
#include <stdio.h>
#include <float.h>
#include <math.h>
#include "phil.h"
#include "register.h"
#include "reg3.h"
#include "quant.h"
#include "reg0.h"
#include "svdcmp.h"
/************************************************************************/
/* FUNCTION: marquar... |
84e9d4641d372c4839b23744ab6873c455c1576c08803dd681447098248a32e2 | C | 9,370 | 343 | //####################################################################
//MILCA
//####################################################################
//2 May 2004
//Contact: kraskov@its.caltech.edu
//####################################################################
//uses mi2c mi2r
#include <stdio.h>
#include <stdli... |
bc4c4d9cc47fafab9e0e425792dc14638d03fac6925e2c080789eb17344fa3d7 | C | 9,384 | 251 |
#include "../headers/fpmain.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"),... |
88231986327ac0c9fbc3b072e82162d3d8f322cf32c132985bb4eff53feeea56 | C | 9,400 | 229 | /* bamtk.c -- main samtools command front-end.
Copyright (C) 2008-2016 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 associated documentation files (the "Software"), to deal
in the Software without re... |
49bc4ac4ee943c9c4d3a3d30a20c3e591c8a507fa9f7e46f8e1dbae954a3fc7c | C | 9,469 | 321 | /* test/split/test_filter_header_rg.c -- split test cases.
Copyright (C) 2014-2016, 2018, 2019 Genome Research Ltd.
Author: Martin O. Pollard <mp15@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"),... |
80f0370a91d82909499b37c5be5004cafa22898122f083ee5827bc6dc2a131b3 | C | 9,817 | 285 | /* cut_target.c -- targetcut subcommand.
Copyright (C) 2011 Broad Institute.
Copyright (C) 2012-2013, 2015, 2016, 2019, 2026 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 associated documentation ... |
1b49d5b5c3f740420c5c2a39dcf9538887f50387795d225c54373819441c12d3 | C | 9,858 | 280 | /* bam.c -- miscellaneous BAM functions.
Copyright (C) 2008-2013, 2015, 2019-2020, 2022, 2025 Genome Research Ltd.
Portions copyright (C) 2009-2012 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 associ... |
48474074ae1c5f53a441a18bf6734ef708156340fcb04c18d8bcb014863f74fc | C | 9,950 | 275 | /* sam_opts.c -- utilities to aid parsing common command line options.
Copyright (C) 2015, 2019, 2025-2026 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 "Sof... |
411cb0ea1ebf069227631a2ecd5854ca5afd9048722f079c75a662a72ed0aae5 | C | 10,142 | 284 | /* test/test-vcf-api.c -- VCF test harness.
Copyright (C) 2013, 2014 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... |
2bfec665e640d3585bc10d6ca364bbf0bda9324f1272f86beb944ea5e3d2ddd6 | C | 10,176 | 316 | /* bam_index.c -- index and idxstats subcommands.
Copyright (C) 2008-2011, 2013-2016, 2018, 2019, 2023-2025 Genome Research Ltd.
Portions copyright (C) 2010 Broad Institute.
Portions copyright (C) 2013 Peter Cock, The James Hutton Institute.
Author: Heng Li <lh3@sanger.ac.uk>
Permission is hereby g... |
85af316291db4c7e11fdabe11cafb4f14755620fb350dbebde534140fa75f751 | C | 10,198 | 392 | //
// fitch.c
// MorPhy2
//
// Created by mbrazeau on 02/05/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#include "morphydefs.h"
#include "mplerror.h"
#include "morphy.h"
#include "fitch.h"
#include "statedata.h"
/**/
int mpl_fitch_downpass
(MPLndsets* lset, MPLndsets* rset, MPLndsets* nset, MPLpa... |
d1bdf266a0f24d1622d65012e000480cd78758ab84f0327b7d0f74b8f52b15b3 | C | 10,228 | 417 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mech_api.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if ... |
d3796346ec8407c066e4cf7ecbf2f74dc159d8e039d60009ca08f3446e096279 | C | 10,459 | 377 | //####################################################################
//MILCA with delay embedding
//####################################################################
//2 May 2004
//Contact: kraskov@its.caltech.edu
//####################################################################
//uses mic_xnyn mir_xnyn
//###... |
ee2ecc41ddbbbb8da7d1c0be386e10ad75ae7a40c84018a14ab5ed8cf6323742 | C | 10,497 | 322 | /* bam_rmdup.c -- duplicate read detection.
Copyright (C) 2009, 2015 Genome Research Ltd.
Portions copyright (C) 2009 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 files (the ... |
da80f0fb355457080ef63ce0d99021c10784e9741208df570a5f766cba6cc6e0 | C | 10,579 | 370 |
#include "../headers/atom.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), t... |
30868d77fde0f7d9496277fbb371fadb920b21fbcd847c787edbd8c653cbb5d8 | C | 10,699 | 282 | /* The MIT License
Copyright (C) 2003-2006, 2008-2010 by Heng Li <lh3lh3@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 restriction, including
without limitati... |
a5ad15cee8f2c47e809ee184614ac8014545779d98b23676e22d65a598830007 | C | 10,710 | 454 | #include "tldefs.h"
#include "treelib.h"
#include "tlerror.h"
#include "tltree.h"
#include "tlutils.h"
#include "tlnewick.h"
#include <stdio.h>
char *tl_read_Newick_brlen(TLflt *brlen, const char* str)
{
char brlenstr[100];
char *c = (char*)str;
int i = 0;
do {
brlenstr[i++] = *c;
++c;... |
ac48677c41acda15107b727741710209941d697e45502f8fb781cb056f4995f1 | C | 10,898 | 377 | /* bam_tview_html.c -- HTML tview output.
Copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Author: Pierre Lindenbaum <plindenbaum@yahoo.fr>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation ... |
1a4f1fa34393011622ac94406345f9edf367284ca4ead6dbc309a6b948b6d23e | C | 11,074 | 379 | /* bam_tview_html.c -- HTML tview output.
Copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Copyright (C) 2019 Genome Research Ltd.
Author: Pierre Lindenbaum <plindenbaum@yahoo.fr>
Permission is hereby granted, free of charge, to any person obtaining a copy
of... |
f4c642f82371f4544bf76d35484b193092cafb54aa6b643c34cfcad1942ed89d | C | 11,134 | 305 | /*<html><pre> -<a href="../libqhull/qh-qhull.htm"
>-------------------------------</a><a name="TOP">-</a>
qvoronoi.c
compute Voronoi diagrams and furthest-point Voronoi
diagrams using qhull
see unix.c for full interface
Copyright (c) 1993-2015, The Geometry Center
*/... |
f3c569ab122fe84a29bf2b9e27856bab520323a75bf5f5f825c99bd6f02e5710 | C | 11,153 | 334 |
#include "../headers/pscoring.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"... |
23fdf64a7167f020385025c2918f4ccd9d4a396764bb0d3c959de0326de77ced | C | 11,208 | 330 | /*<html><pre> -<a href="../libqhull/qh-user.htm"
>-------------------------------</a><a name="TOP">-</a>
user_eg.c
sample code for calling qhull() from an application
call with:
user_eg "cube/diamond options" "delaunay options" "halfspace options"
for example:
user_... |
44a4b62c32917524af4e592efd93e75483a131d6f4d210482e24b919e459802e | C | 11,376 | 326 | /*<html><pre> -<a href="../libqhull_r/qh-user_r.htm"
>-------------------------------</a><a name="TOP">-</a>
user_eg_r.c
sample code for calling qhull() from an application. Uses reentrant libqhull_r
call with:
user_eg "cube/diamond options" "delaunay options" "halfspace op... |
c54896ca8102cfc643020644496f498d171ca16dedfae63ec285e56c36862cf9 | C | 11,488 | 462 | #include "../headers/aa.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to d... |
df761ccbb012e3ff83225b808fc3925c996e0c0a25d43c71d5de3af0675f9e81 | C | 11,490 | 453 | // interp4_table1_adj.c
// 4D periodic interpolation using table lookup: adjoint.
//
// forward direction: (for m = 1,...,M)
// f(t_m) = \double_sum_{k1,2,3,4=0}^{K1,2,3,4-1} c[k1,k2,k3,k4]
// h_1( (t_m1 - k1) mod K1 ) h_2( (t_m2 - k2) mod K2 ) h_3( (t_m3 - k3) mod K3 ) h_4( (t_m4 - k4) mod K4 )
//
// adjoint direction... |
be8d009b5bb87b9db8472308a78a91ef3a9cd74d7ff4eedc2c97c235629bed4b | C | 11,535 | 502 |
#include "../headers/memhandler.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Softwar... |
15e77e0d5b2a80b7617762239ab6c6a23edc7d0924ff25c968ed2dc667bc2a79 | C | 11,538 | 311 | /* bgzip.c -- Block compression/decompression utility.
Copyright (C) 2008, 2009 Broad Institute / Massachusetts Institute of Technology
Copyright (C) 2010, 2013-2016 Genome Research Ltd.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentat... |
d1c094b6d27b1584226f4d03a52e7934e67212d046b9fa9992cfe3586d886a26 | C | 11,585 | 350 | #include "../headers/write_visu.h"
/*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software... |
0fe49eddb541248306f05cfcd7c4e8683d81b63d00d97d0472949adba40c72bc | C | 11,603 | 360 | /* bam_rmdup.c -- duplicate read detection.
Copyright (C) 2009, 2015, 2016, 2019, 2026 Genome Research Ltd.
Portions copyright (C) 2009 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 documen... |
08636336ee30e6d4411ed8a873a7347a537a9d86b38d8b6879a1f8aabdd6e966 | C | 11,608 | 316 | /*<html><pre> -<a href="../libqhull/qh-qhull.htm"
>-------------------------------</a><a name="TOP">-</a>
qhalf.c
compute the intersection of halfspaces about a point
see unix.c for full interface
Copyright (c) 1993-2015, The Geometry Center
*/
#include "libqhull/libqhul... |
ec52a18c7c22df9986cfa3b68af75e150fa86b231524ee59203360292fdb2afe | C | 11,635 | 315 | /*<html><pre> -<a href="../libqhull/qh-qhull.htm"
>-------------------------------</a><a name="TOP">-</a>
qdelaun.c
compute Delaunay triangulations and furthest-point Delaunay
triangulations using qhull
see unix.c for full interface
Copyright (c) 1993-2015, The Geome... |
60ecfcc5f881a6a6142ff1f1361cc87b0a37a333d7fb4ced6d4d9156dd3d6fe2 | C | 11,702 | 251 | /* The MIT License
Copyright (c) 2011 Heng Li <lh3@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 restriction, including
without limitation the rights to use,... |
a49d010491dff9c8abd2729ce67484f459106184e8dab034b8737681366deef3 | C | 11,702 | 414 | /*
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,
... |
244030330122b73585cde729c02b1f031508b33d9f7e07c36ae11d0c04c399b0 | C | 11,710 | 318 | /*<html><pre> -<a href="../libqhull/qh-qhull.htm"
>-------------------------------</a><a name="TOP">-</a>
qhalf.c
compute the intersection of halfspaces about a point
see unix.c for full interface
Copyright (c) 1993-2015, The Geometry Center
*/
#include "libqhull_r/libqh... |
419ee8a1d11b6307ab7539cb5c6f8aaa83542aaed0d32b6c51321626c3f79072 | C | 11,733 | 317 | /*<html><pre> -<a href="../libqhull/qh-qhull.htm"
>-------------------------------</a><a name="TOP">-</a>
qdelaun.c
compute Delaunay triangulations and furthest-point Delaunay
triangulations using qhull
see unix.c for full interface
Copyright (c) 1993-2015, The Geome... |
671b8a46d28c6704a71bf072f8b943b7d75fe7a05f7384ed5e6f0540dd2a2e31 | C | 11,766 | 484 | // interp4_table1_for.c
// 4D periodic interpolation using table lookup.
//
// forward direction: (for m = 1,...,M)
// f(t_m) = \double_sum_{k1,2,3,4=0}^{K1,2,3,4-1} c[k1,k2,k3,k4]
// h_1( (t_m1 - k1) mod K1 ) h_2( (t_m2 - k2) mod K2 ) h_3( (t_m3 - k3) mod K3 ) h_4( (t_m4 - k4) mod K4 )
//
// adjoint direction: (for k1... |
3e008abae347d53bec776fa8822799385b398bc0e9ac95a5807c153c9904a3ab | C | 11,850 | 377 | /*
*! @title Wifi spike monitoring
*! @file app_main.cpp
*! @author Romain Beaubois
*! @date 20 Apr 2023
*! @copyright
*! SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
*! SPDX-License-Identifier: GPL-3.0-or-later
*! @brief
*! Wifi spike monitoring
*! * Wifi AP : esp as wifi... |
965b65c8b6b8bb867ca2879223deac276ed034ce6affeb9e948808aae2171166 | C | 11,873 | 318 | /*<html><pre> -<a href="../libqhull/qh-qhull.htm"
>-------------------------------</a><a name="TOP">-</a>
qvoronoi.c
compute Voronoi diagrams and furthest-point Voronoi
diagrams using qhull
see unix.c for full interface
Copyright (c) 1993-2015, The Geometry Center
... |
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