sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
56f15a11c4b190a48afa7bdade56f13f06e40405db5db44e3610c01db028e25e | C | 1,434 | 63 | #include<pandaseq-plugin.h>
#include<stdlib.h>
HELP("Produce statistics on the overlaps examined. Somewhat interesting to see the efficiency of the k-mer table.", "overlap_stat");
VER_INFO("1.0");
struct data {
PandaWriter writer;
size_t counts[];
};
static bool check_func(
PandaLogProxy logger,
const panda_res... |
995ef1c3ea0685ea88d01e1aaedf705e45f1591c8a9fb6ede718b572d9758084 | C | 1,434 | 38 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpccm.h"
/****************************************************************************... |
9cd920ba827eb0f31a4789130c5fb91f363385e60285f14dc06e8d6081638b65 | C | 1,442 | 43 | /// @file branch.c
/// @author Vesa Oikonen
/// @brief Isotope branching ratio correction.
///
/******************************************************************************/
#include "libtpcmisc.h"
/******************************************************************************/
/*************************************... |
8af53918c7c86461418e46634ae04f656217ef8d64594635e6002c36bfb58568 | C | 1,446 | 40 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpcimage.h"
/*************************************************************************... |
1da885081ef2996edaf0c3495f8bfecff2110eb104946248f7ce53d28ed471b0 | C | 1,450 | 38 | #include "common.h"
#include "cart.h"
void cartEdit7(struct cart *cart)
{
// since spliceAI got turned from a super track into a composite track and the browser saves the default state of subtracks of supertracks into
// sesssions, which unfortunately will turn on the new composite spliceAI track if set, we need to ... |
db86ea7f9b467b3a6b089b8645a51b12614295c7a555e5aa3e856a8006a2c959 | C | 1,453 | 62 | /* bedToBinDex - Convert bed file to binary and index it. */
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "bed.h"
void u... |
c84df2115e958dc370dd2876c8673dfb5675714e4871998045d956488c493f46 | C | 1,455 | 65 | /* ooCloneSizes - Print out sizes of a bunch of clone .fa files. */
#include "common.h"
#include "portable.h"
#include "linefile.h"
#include "dnaseq.h"
#include "fa.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"ooCloneSizes - Print out sizes of a bunch of clone .fa files.\n"
"Also first and last frag... |
6495424a6fdae9f081cb2a7e78b2d968fbee70c0207cfc3c5a6c6e040d8b0801 | C | 1,457 | 40 | #include "cs_mex.h"
/* cs_sqr: symbolic sparse QR factorization */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double s ;
css *S ;
cs Amatrix, *A ;
int m, n, order, *p ;
if (nargout > 7 || nargin != 1)
{
mexErrMsgTxt ("U... |
6140ee2651ab198716fb80756d9219b1654bc971496acb8b98725e6c045dea3f | C | 1,460 | 55 | /* cdwFixCdwFileNamePath - Fix case where root path included in cdwFileName. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "jksql.h"
#include "cdw.h"
#include "cdwLib.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"cdwFixCdwFileNamePath - Fix case where root ... |
17ff819e8cf4bea2924f9e5562c76e3d961c553c9d57357175853cde43a25e55 | C | 1,464 | 68 | #include<stdio.h>
#include<pandaseq-plugin.h>
HELP("Filters sequences based on the contents of a file of ids, one sequence ID per line.", "filter:file");
VER_INFO("1.0");
static bool precheck_func(
PandaLogProxy logger,
const panda_seq_identifier *id,
const panda_qual *forward,
size_t forward_length,
const pand... |
1f604cf52e1f1e6e5f91687769d3bc621645dc921e491f14ff91656441de0f40 | C | 1,464 | 66 | /* agxToBed program that merges all exons in an altGraphX
structure to form a bed.
*/
#include "common.h"
#include "altGraphX.h"
#include "obscure.h"
void usage()
{
errAbort("agxToBed - Utility program that condenses an altGraphX record\n"
"into a bed record.\n"
"usage:\n\t"
"agxToBed altGraphXFile bedOutFil... |
073a56e3168b8cd0e18d7377257647b6df6bf8967662f67abaafdfc930a1a6b7 | C | 1,469 | 71 | /* Currently unused... */
/* eztok - simple but often effective tokenizer. Separates
* things into space or punctuation delimited words. Punctuation
* (anything non-alphanumeric) is returned as a single character
* token. It will handle quotes, but not allow escapes within
* quotes. */
#include "common.h"
#inc... |
aaf69b61788235712734cbcc4024a1a05726ec02fc13d7216fe1f220f5b799bc | C | 1,469 | 40 | #include "cs_mex.h"
/* cs_sqr: symbolic sparse QR factorization */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double s ;
cs_dls *S ;
cs_dl Amatrix, *A ;
CS_INT m, n, order, *p ;
if (nargout > 7 || nargin != 1)
{
mexErrM... |
1a0849b610bf0996744de576317c63e3f8721538ed57034819da7e851fffb50d | C | 1,472 | 41 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpctac.h"
/***************************************************************************... |
2b9023334646326207c68f47213766b91d5faf69ded76af34c4ec13c1c2c6caa | C | 1,472 | 61 | /*
* Copyright (c) by Peter De Rijk (VIB - University of Antwerp)
* See the file "license.txt" for information on usage and redistribution of
* this file, and for a DISCLAIMER OF ALL WARRANTIES.
*/
#define _FILE_OFFSET_BITS 64
#define _GNU_SOURCE
#include "cg.h"
#include <stdio.h>
#include <stdlib.h>
#include <st... |
2a1e9c0f7f33fcf72c67e9fd7e3af60e8f01ac11b5f5da40a21b6d32a34dbcc2 | C | 1,474 | 34 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
daf5cd57cda26021d0fd09cbd73a266f8ae82f3c68b0041071a829fce55fc1a7 | C | 1,477 | 37 | /// @file recovery.c
/// @brief Functions for computing recovery errors for vessel.
/// @author Vesa Oikonen
///
/*****************************************************************************/
#include "libtpcidi.h"
/*****************************************************************************/
/**************... |
0c393d7ea14084cc487b362d5f029f743e98c693243f5acd92eab084210dc7b2 | C | 1,480 | 63 | /* fakeOut - fake a RepeatMasker .out file based on a N's in .fa file. */
#include "common.h"
#include "fa.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"fakeOut - fake a RepeatMasker .out file based on a N's in .fa file\n"
"usage:\n"
" fakeOut x.fa.masked x.fa.out\n");
}
void fakeOut(char *inNam... |
faabc2bd3081475cc40ee27d6a2bfa53e260b677ae79aff8baa852c007798116 | C | 1,484 | 65 | /* cdwFixDoubleHivePath - Fix double inclusion of hive path in cdwSubmit URLs.. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "jksql.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"cdwFixDoubleHivePath - Fix double inclusion of hive path in cdwSubmit URLs.\n"... |
8d8142bd889ff173a87c1e246b56be36899125a18352d7611097e5b8972ebd74 | C | 1,487 | 50 | /* clickOnImage - handle click on image. Calculate position in genome
* and forward to genome browser. */
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hash.h"
#include "jksql.h"
#i... |
c2f57dae1356c892e8a6452cb4d062a38cc6ab372fc7638f3c360f92a186853f | C | 1,488 | 55 | /* cdwAddQaContamTarget - Add a new contamination target to warehouse.. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "... |
d15a1400fde9266ab259ff9a7fb8782896e271d5f3b5b89c3cc267f5da0a842c | C | 1,498 | 61 | #include <stdio.h>
#include <stdlib.h>
#include "bgzf.h"
#include "bam.h"
#define BUF_SIZE 0x10000
int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
{
BGZF *fp;
bam_header_t *old;
int len;
uint8_t *buf;
if (in->open_mode != 'r') return -1;
buf = malloc(BUF_SIZE);
old = bam_header_read(in);
fp = bgzf_f... |
a58f8dcc2493fc380c649212538e840d15c46ad1b9e033411528e67035800199 | C | 1,500 | 60 | /* object - handle runtime objects. Do reference
* counting and automatic cleanup. */
#include "common.h"
#include "../compiler/pfPreamble.h"
#include "runType.h"
void _pf_var_link(_pf_Var var)
/* Increment _pf_refCount if variable needs cleanup. */
{
struct _pf_type *type = _pf_type_table[var.typeId];
if (type->ba... |
25b2fff50bf61a7192dc8f4b89ae0fcd4b1ef93f7412025d569d518d85d1bd8e | C | 1,504 | 59 | /*
* Copyright (c) by Peter De Rijk (VIB - University of Antwerp)
* See the file "license.txt" for information on usage and redistribution of
* this file, and for a DISCLAIMER OF ALL WARRANTIES.
*/
#define _FILE_OFFSET_BITS 64
#define _GNU_SOURCE
#include "cg.h"
#include "tools.h"
#include <stdio.h>
#include <std... |
d97e507c3d45f9e1a82b4e8976a4f86ebb1e70f92a7e2b28a2a3e994a46baa20 | C | 1,504 | 55 | /* edwAddQaContamTarget - Add a new contamination target to warehouse.. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "... |
c5952ae814f5efb63f4e1a6d8cf9e5dd5e4c7271eaa0582500cebcff05c8a05b | C | 1,507 | 66 | /* bedToBaseMask - write bed file as baseMask */
/* Copyright (C) 2008 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "bed.h"
#include "genomeRangeTreeFile.h"
#include "options.h"
/* FIXME:
* - would be n... |
801618e99a7d7a4dd87a4dbfac2d8ff203ec9ff45fe82cb25f9173fb862cb9a3 | C | 1,514 | 71 | /* bedThickOnly - Reduce bed to just thick parts.. */
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "bed.h"
void usage()
... |
0a205f1147d928f66fdc9afff8ce6911460fd86d9d8c48a3243e0c4b80160731 | C | 1,517 | 61 | #include "wtime.h"
#include <stdlib.h>
/* Prototype */
void wtime( double * );
/*****************************************************************/
/****** E L A P S E D _ T I M E ******/
/*****************************************************************/
double elapsed_time( void )
{
... |
36e531240b2b6bf13a37a55c7b46ec55ffd3ccf5f70574f036e3b8561a3b522b | C | 1,526 | 42 | #include <assert.h>
#include <ctype.h>
#include <stdlib.h>
#include <zlib.h>
#include <stdio.h>
#include <unistd.h>
#include "sickle.h"
#include "kseq.h"
void print_record (FILE *fp, kseq_t *fqr, cutsites *cs) {
fprintf(fp, "@%s", fqr->name.s);
if (fqr->comment.l) fprintf(fp, " %s\n", fqr->comment.s);
els... |
90ca62c08ca403d1b7dace246d56a3b75ced43f1a34c6148728a6d5bd2db09ba | C | 1,529 | 45 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
c25fa690de2745c6a4d89b37759bfbff9453dece45b7815e2e2dba2dacf3e381 | C | 1,529 | 57 | /* cdwUndeprecate - Undeprecate a list of file accessions.. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "cdw.h"
#include "cdwLib.h"
#include "obscure.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"cdwUndeprecate - Undeprecate a list of file accessions.\n"
... |
304d2f516b03189c67d895fab0c691573cb4ce33a50efaae6fbac7e585da3523 | C | 1,533 | 60 | #include "cs_mex.h"
/* A = cs_frand (n,nel,s) creates an n-by-n sparse matrix consisting of nel
* finite elements, each of which are of size s-by-s with random symmetric
* nonzero pattern, plus the identity matrix.
* See also MATLAB/Demo/private/frand.m */
static
cs *cs_frand (int n, int nel, int s)
{
int ss = ... |
c639919f50b26ba53a27511850a44c482a0a44d10332f4a54c56c36db10ded0d | C | 1,535 | 48 | #include "cs_mex.h"
/* cs_cholsol: solve A*x=b using a sparse Cholesky factorization */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
CS_INT order ;
if (nargout > 1 || nargin < 2 || nargin > 3)
{
mexErrMsgTxt ("Usage: x = cs_cholsol(A... |
3a8b762a35d788c67f1fdb1efe970ce6aab0edc42532488be556345d4b28fd2a | C | 1,536 | 44 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
98bb1cc91ae3db624da46c1e048692c450e14f585149601e2a91d25240f362c0 | C | 1,536 | 79 | #include "../verrou.h"
#include <stdio.h>
#include <math.h>
#include <stdbool.h>
#include <string.h>
float compute () {
float res=0;
int i;
for(i=0; i< 1000; i++){
res+=(float)0.1;
}
return res-100 ;
}
int main (int argc, char** argv) {
double x=cos(42.); if(x!=x) printf ("FAILURE\n");// line to forc... |
17340357a436f0f7a00f48515dc54299e91eed1173e9bd9c385eb750d92336ed | C | 1,542 | 91 | #include <math.h>
#include <stdio.h>
#include <stdlib.h>
#define bit(A, i) ((A >> i) & 1)
typedef unsigned long long int u_64;
typedef unsigned int u_32;
static void print_double(double d) {
u_64 a = *((u_64 *)&d);
for (int i = 63; i >= 0; i--)
(i == 63 || i == 52) ? printf("%lld ", bit(a, i))
... |
c422344898b5693112c8fac1a3d2efff91f72588c517d1777dc7edc861a99310 | C | 1,545 | 57 | /* edwUndeprecate - Undeprecate a list of file accessions.. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "encodeDataWarehouse.h"
#include "edwLib.h"
#include "obscure.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"edwUndeprecate - Undeprecate a list of file... |
3c735570609aa009dad2498c122b1b4f1fee800681330d356ff942215f0880a2 | C | 1,560 | 40 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
888286debb7cd95def92d4ad1ccbd7bd3d9b96c62b75958579bab0e2c0a1bfb8 | C | 1,560 | 69 | /* Check out - check directory to make sure it has
* a .out file for each .fa file, and that .out file
* is non-empty. */
#include "common.h"
#include "hash.h"
#include "portable.h"
void checkOut(char *dir)
/* Check out - check directory to make sure it has
* a .out file for each .fa file, and that .out file
* is... |
8447bf440b20ecf73afb74c3dee5a64209e6d36c9f1377017884782728510e87 | C | 1,562 | 47 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
657ce2f244d64fb6727f2218057263990869db3e08f9879af9d8306bdd1721ad | C | 1,567 | 35 | #include "cs.h"
/* C = A*B */
cs *cs_multiply (const cs *A, const cs *B)
{
int p, j, nz = 0, anz, *Cp, *Ci, *Bp, m, n, bnz, *w, values, *Bi ;
double *x, *Bx, *Cx ;
cs *C ;
if (!CS_CSC (A) || !CS_CSC (B)) return (NULL) ; /* check inputs */
if (A->n != B->m) return (NULL) ;
m = A->m ; anz = A... |
6841b1999dbe9914500b449724fb577ca7fe55ededa505634968658148d307b7 | C | 1,574 | 39 | /* PANDAseq -- Assemble paired FASTQ Illumina reads and strip the region between amplification primers.
Copyright (C) 2011-2012 Andre Masella
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 Fou... |
7004773cd7ba78938a3173fa66d167818c7be9504276cbd219444f39374e887a | C | 1,577 | 35 | #include "cs.h"
/* C = A*B */
cs *cs_multiply (const cs *A, const cs *B)
{
CS_INT p, j, nz = 0, anz, *Cp, *Ci, *Bp, m, n, bnz, *w, values, *Bi ;
CS_ENTRY *x, *Bx, *Cx ;
cs *C ;
if (!CS_CSC (A) || !CS_CSC (B)) return (NULL) ; /* check inputs */
if (A->n != B->m) return (NULL) ;
m = A->m ; an... |
51ca879f514d4cec421909f9cbd0efd1326a8b7767a279a1c80f9c2d557bc5ba | C | 1,581 | 53 | /* code to support suggesting genes given a prefix typed by the user. */
/* Copyright (C) 2014 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "suggest.h"
char *connGeneSuggestTable(struct sqlConnection *conn)
// return name ... |
65f62d255dba71ca1c3990d0ffe0986132ddd298b3c904d6920fc9ccb48a3fac | C | 1,584 | 42 | /** @file niftiname.c
* @brief Procedures for NIfTI file names.
*/
/*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcnifti.h"
/****************************************... |
b0fcdd2c15e4897a4356dfc549754c4380a792f1333d2dc7285d335017c62a05 | C | 1,584 | 46 |
// Code to parse list of exported data track hubs from table and print as browser dialog
// for client dialog (js)
//
/* Copyright (C) 2024 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "dystring.h"
#... |
9bc19f45fbd2624a1a24e53b4cdc75304c22e45a4786838da70f5d2181f286fe | C | 1,592 | 59 | #include "cs_mex.h"
/* A = cs_frand (n,nel,s) creates an n-by-n sparse matrix consisting of nel
* finite elements, each of which are of size s-by-s with random symmetric
* nonzero pattern, plus the identity matrix.
* See also MATLAB/Demo/private/frand.m */
cs_dl *cs_dl_frand (CS_INT n, CS_INT nel, CS_INT s)
{
C... |
8d63b45edf0a1ca6a82c18738be919d320f4c60b63c5fa773a2122636454df36 | C | 1,596 | 56 | #include "cs_mex.h"
/* cs_thumb: convert a sparse matrix to a dense 2D thumbnail matrix of size
* at most k-by-k. k defaults to 256. A helper mexFunction for cspy. */
#define INDEX(i,j,lda) ((i)+(j)*(lda))
#define ISNAN(x) ((x) != (x))
#ifdef DBL_MAX
#define BIG_VALUE DBL_MAX
#else
#define BIG_VALUE 1.7e308
#endif
... |
9529975d5a807a83c62b75dc6df028503892d675da44dd9fd3431e22ad91f8f6 | C | 1,600 | 48 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
4bbbafb7b40ba2739a2aa5e6d96bfa5c7aa32f5526ef9608519ada5d5b8ab23e | C | 1,606 | 45 | #include "cs_mex.h"
/* cs_droptol: remove small entries from A */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
CS_INT j, k ;
double tol ;
if (nargout > 1 || nargin != 2)
{
mexErrMsgTxt ("Usage: C = cs_droptol(A,tol)") ;
}
... |
b11401e758890f2c3addcc274acc5a29d1edf29a26c9d60c0a4ac50b8955d5f0 | C | 1,614 | 72 | /* agpCloneList - Make simple list of all clones in agp file. */
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "cheapcgi.h"
boolean ver = FALS... |
b2f1a60901c49cc1adf497a9ca45a7e970009cd4175224a42bf521b727577506 | C | 1,614 | 65 | #include "../verrou.h"
#include <stdio.h>
#include <math.h>
#include <stdbool.h>
#include <string.h>
float compute () {
float res=0;
int i;
for(i=0; i< 1000; i++){
res+=(float)0.1;
}
return res-100 ;
}
void detect(int index, float* res, float res_init){
printf("res[%d] ",index);
if((res[index] - ... |
b671171c504d7d98ea0567fa19fe95df317a09b6e6bf3ef076bd89754188a31d | C | 1,614 | 73 | #include "../verrou.h"
#include <stdio.h>
#include <string.h>
#include <math.h>
int N = 100000;
float epsilon = 1e-9;
float compute () {
float sum = 1;
int i;
VERROU_START_INSTRUMENTATION;
for (i = 0 ; i < N ; ++i) {
sum += epsilon;
}
VERROU_STOP_INSTRUMENTATION;
return sum;
}
int main (int argc, ... |
2aa1fc19bee393cb4186f344983ddd9da377b986c4088285793c36d6fd15beda | C | 1,615 | 92 | #include <math.h>
#include <stdio.h>
#include <stdlib.h>
#define bit(A, i) ((A >> i) & 1)
typedef unsigned long long int u_64;
typedef unsigned int u_32;
static void print_double(double d) {
u_64 a = *((u_64 *)&d);
printf("\t\t");
for (int i = 63; i >= 0; i--)
(i == 63 || i == 52) ? printf("%lld ", bit(a,... |
beb7716d2afc88109c8e2ded1e8bd661bd046f626dcdcb2e1782919b93e95839 | C | 1,616 | 57 | #include "cs.h"
/* test real/complex conversion routines (int version) */
int main (void)
{
cs_cl *T, *A, *A1, *A2, *B ;
cs_dl *C1, *C2, *Treal, *Timag ;
printf ("\n--- cs_ldemo, size of CS_INT: %d\n", (int) sizeof (CS_INT)) ;
T = cs_cl_load (stdin) ; /* load a complex triplet matrix, T */
... |
d4a6f31ceea279d25fe34a710b6a483e9e00fb48a8a81afd98bc00b5b14b6a39 | C | 1,616 | 57 | #include "cs.h"
/* test real/complex conversion routines (int version) */
int main (void)
{
cs_ci *T, *A, *A1, *A2, *B ;
cs_di *C1, *C2, *Treal, *Timag ;
printf ("\n--- cs_idemo, size of CS_INT: %d\n", (int) sizeof (CS_INT)) ;
T = cs_ci_load (stdin) ; /* load a complex triplet matrix, T */
... |
fc6f235d27aa9e5c615b783956cb33230827324428ae5785905f9a2a2e00e133 | C | 1,617 | 54 | /* edwScriptSubmit - Handle submission by a script via web services.. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "che... |
588cf9736f0f329f310a5f3683be41058a33e3a62e4471614db311675e53359b | C | 1,618 | 60 | /* col gsidSubjInfo - columns having to do with subjInfo and closely related tables. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "dystring.h"
#include "jksql.h"
#include "gsidTa... |
e1f0289d01192f30454a3a88070ec4c78ac5fb6dbe01a9cae76410852316dd42 | C | 1,619 | 62 | /* cdwFixUpdateTime - Change update times in warehouse to match those in cdwFile table.. */
#include "common.h"
#include <sys/types.h>
#include <utime.h>
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "errAbort.h"
#include "jksql.h"
#include "cdw.h"
#include "cdwLib.h"
void usage()
/* Explain us... |
b2d69c88378a12e8b9af1ce494f545be7384ecb6b52621e1ec2cb9aa57464785 | C | 1,624 | 36 | #include "cs.h"
/* depth-first-search of the graph of a matrix, starting at node j */
int cs_dfs (int j, cs *G, int top, int *xi, int *pstack, const int *pinv)
{
int i, p, p2, done, jnew, head = 0, *Gp, *Gi ;
if (!CS_CSC (G) || !xi || !pstack) return (-1) ; /* check inputs */
Gp = G->p ; Gi = G->i ;
... |
a9f50bcc32e4302ff0bd5f32352ced76b6b42709118fe0bc5fe4701f1f0dac61 | C | 1,627 | 46 | #include "cs.h"
/* print a sparse matrix */
CS_INT cs_print (const cs *A, CS_INT brief)
{
CS_INT p, j, m, n, nzmax, nz, *Ap, *Ai ;
CS_ENTRY *Ax ;
if (!A) { printf ("(null)\n") ; return (0) ; }
m = A->m ; n = A->n ; Ap = A->p ; Ai = A->i ; Ax = A->x ;
nzmax = A->nzmax ; nz = A->nz ;
printf ("CXSp... |
1eb676387736c8c5906c55e9e5f909f50c48c76ee0877d56edd5897c9638251c | C | 1,634 | 87 | #include "quadmath_stats.h"
#include <assert.h>
#include <math.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#ifndef DEBUG
#define DEBUG 0
#endif
/* Computes the means */
FP128 compute_mean(const int N, const FP128 data[]) {
assert(N >= 1);
FP128 sum = data[0];
FP128 c = 0.0, y, t;
int i;
... |
d184a2b427ec6daa3fca6a55a0011c0632d17bf22cb14dae36a3f573c796e745 | C | 1,645 | 36 | #include "cs.h"
/* depth-first-search of the graph of a matrix, starting at node j */
CS_INT cs_dfs (CS_INT j, cs *G, CS_INT top, CS_INT *xi, CS_INT *pstack, const CS_INT *pinv)
{
CS_INT i, p, p2, done, jnew, head = 0, *Gp, *Gi ;
if (!CS_CSC (G) || !xi || !pstack) return (-1) ; /* check inputs */
Gp = G-... |
08bb169eaa1b744f6a2cd2f910366844f03231eb3e65c358db100991daca2104 | C | 1,647 | 64 | /* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "sample.h"
void usage()
{
errAbort("scaleSampleFiles - scale all of the scores in a file by a scale factor.\n"
"usage:\n\t"
"scaleSa... |
55bd75db0888449f2c0aed609a11528734c517bc9a1fe19e7957e090de1e985c | C | 1,649 | 46 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2012-2018 OpenFOAM Foundation
\\... |
ef835274dae2a327cf4b4c1bfb21948ef466bda4742643452a5612d0ef1f5e62 | C | 1,650 | 47 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
073b2f7b752713362c282641b9bf7af12f246427ea126abf8bcd1f73d5a7ec76 | C | 1,653 | 40 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2013-2018 OpenFOAM Foundation
\\... |
3f5645e1a7065ddbf3e2cd3d2cbc2e66746d27055deb9990618d8af99654c4a3 | C | 1,653 | 91 | #include "common.h"
#include "cheapcgi.h"
#include "htmshell.h"
int noneOrNumber(char *s)
{
return atoi(s);
}
void dustProt(char *in,char *out)
{
char c;
while ((c = *in++) != 0)
{
if (isalpha(c)) *out++ = c;
}
*out++ = 0;
}
void formatOutput(char *output, int spacer, int liner,
boolean showNumbers, c... |
e475f6134adf9f57ebf14494c55d35d51a9b6031ed7f2ffe0d1ed1983e4d5390 | C | 1,656 | 51 | /* Regression test: the size --inst-func reports for a pointer argument that is
* forwarded from the caller's own argument must hold for every caller.
*
* The size is fixed at compile time for a call site, but the backend reads and
* rounds that many elements whichever caller supplied the pointer. It must
* theref... |
e5f522f51098eb0b5e833c921fbe4018cf9892bc265a1878407521649b94f142 | C | 1,657 | 52 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
390fa51def9ffd1d9251ba6c6e4373e45f35541385fea2e2e6a187261e5eafc8 | C | 1,660 | 63 | /*
* Copyright (c) by Peter De Rijk (VIB - University of Antwerp)
* See the file "license.txt" for information on usage and redistribution of
* this file, and for a DISCLAIMER OF ALL WARRANTIES.
*/
#define _FILE_OFFSET_BITS 64
#define _GNU_SOURCE
#include "cg.h"
#include <stdio.h>
#include <stdlib.h>
#include <st... |
46ee6f0feadd5afa5dffa428568a21177a5e921315c8201bcbf00c3f5b4714e8 | C | 1,662 | 51 | #include "cs_mex.h"
/* cs_permute: permute a sparse matrix */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
CS_INT ignore, *P, *Q, *Pinv, m, n ;
if (nargout > 1 || nargin != 3)
{
mexErrMsgTxt ("Usage: C = cs_permute(A,p,q)") ;
}
... |
961713c933e1a2ba885241ce658e7b8011f5adba704fd5192e1013d195adc439 | C | 1,662 | 43 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) YEAR OpenFOAM Foundation
\\/ ... |
9611fc03f6c3fd4425e08965f06daf2cc79392938b5656b4445d5981b859aa1c | C | 1,670 | 52 | /* Copyright (C) 2012 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "cheapcgi.h"
#include "hgTrackUi.h"
#include "jksql.h"
#include "hdb.h"
#include "hui.h"
#include "trackDb.h"
#include "customTrack.h"
#in... |
7e3f592102abe11357e64fe8b82e0f56dc8f51a531619afa360f3ef2037720c2 | C | 1,676 | 90 | #include "common.h"
#include "heap.h"
int randomVals[] = { 2, 2, 50, 100, -1, 0, 8, 8, 5, 10, };
struct slInt {
/* list of ints, should probably switch to slRef but harder to debug */
struct slInt *next;
int val;
};
int slIntCmp(const void *va, const void *vb)
/* Compare based on val. */
{
const struct ... |
e002a0af5a77e2d468c553df945d3057071a24a52ce63f47314f5a7851696217 | C | 1,685 | 72 | /* Copyright (C) 2010 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "jksql.h"
#include "hgTracks.h"
#include "rnaPLFoldTrack.h"
/* ------ BEGIN wiki ------ */
/********************************************... |
5aaa020151a91dcf109c1d1b46a634bb5a1d9a5df6cfe793b6c1f866b4bb226c | C | 1,688 | 46 | #include "cs_mex.h"
/* cs_qr: sparse QR factorization */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
css *S ;
csn *N ;
cs Amatrix, *A, *D ;
int m, n, order, *p ;
if (nargout > 5 || nargin != 1)
{
mexErrMsgTxt ("Usage: [V... |
94c3a9a5ca544a830650b6b0f4f92f28faa5b5b7f867aa53209dc4f70e3d92da | C | 1,692 | 48 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpcnifti.h"
/*************************************************************************... |
beea26363eda95a8a0be31441cb12d64c983cf3cc7fe665c5f3d313dfec2dacd | C | 1,695 | 78 | /*
*
* Copyright (C) 2006-2007, Robert Oostenveld
*
* This implements C = A * B for uint64 data types
* and either A and B have the same size or one of them is scalar.
*
* This function does not check the occurence of integer overflowing.
*
*/
#include <math.h>
#include "mex.h"
void
mexFunction (int nlhs, mx... |
d467f57dda152a26d5b26f3649653e2cf64e94767c0e58a682fb92a33a6673a7 | C | 1,698 | 52 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
959d412fa21edebf8318c42f02e3dc1402b822baaea32129135bff9e941d6aa5 | C | 1,700 | 46 | #define _POSIX_C_SOURCE 2
#include<ctype.h>
#include<stdbool.h>
#include<stdio.h>
#include<stdlib.h>
#include<string.h>
#include<unistd.h>
#include "config.h"
#include "pandaseq.h"
typedef struct {
const char *str;
int dir;
PandaIdFmt format;
panda_seq_identifier id;
} test_case;
bool check(
const test_case * te... |
a304a2664f7fe1b49a360d783c2cecd8f2fc3ead974d3cfd0c6f19c879345a11 | C | 1,700 | 74 | #include <sys/types.h>
#include <fcntl.h>
#include <sys/mman.h>
#include <sys/syssgi.h>
#include <sys/immu.h>
#include <errno.h>
#include <stdio.h>
/* The following works on SGI Power Challenge systems */
typedef unsigned long iotimer_t;
unsigned int cycleval;
volatile iotimer_t *iotimer_addr, base_counter;
double r... |
3329358621d60419dc409d53089aa46977aaf9fce07367294255eb30a92c9cac | C | 1,704 | 43 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
05ba0df159fc4343bd22edc5e8b4e98f521485bd1f80bb5e5b1bbdc4f9fbd8a8 | C | 1,707 | 71 | /* checkPsl - make sure all the psls that should be there are there
* and are not empty. */
#include "common.h"
#include "portable.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"checkPsl - make sure all psls that should be there are there\n"
"and are not empty.\n"
"usage:\n"
" checkPsl inLstDi... |
353f3777d8113a26b28a730573ed20f88e8a19d288e360ad95c38b0c1640fe99 | C | 1,710 | 62 | /* oregannoUi.c - char arrays for oreganno UI features */
/* Copyright (C) 2014 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "oregannoUi.h"
#include "common.h"
/* some stuff for mutation type choices */
/* labels for checkb... |
91a1ca3b57ead56a7c56c9d3fa0154ca420ccf026f9ad8b72677ad03d07e379c | C | 1,718 | 70 | #include "common.h"
#include "bed.h"
#include "options.h"
boolean cdsOnly = FALSE;
void usage()
{
errAbort("bedToExons - Split a bed up into individual beds.\n"
"One for each internal exon.\n"
"usage:\n "
"bedToExons originalBeds.bed splitBeds.bed\n"
"options:\n"
" -cdsOnly - Only output the coding por... |
a78a2b90960dcf06c16e863356bb9586441dc4d089d1a79453ec6ee8445ced9c | C | 1,719 | 69 | /* bedToGenePred - convert bed format files to genePred format */
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "options.h"
#include "bed.h"
#include "genePred.h"
#include "linefile.h"... |
b9698a82961db4dd20f0e7b4b02f78e929be3b3e3aae1bf5bec7fb6750c57c91 | C | 1,725 | 46 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2014-2018 OpenFOAM Foundation
\\... |
ee940bd7e17ee170970f74ddaabb32e535fe4df0ce21fc0477aeff08b182b1fc | C | 1,725 | 65 | /* cdwFix5 - Fix problem where .vcf.gz files lost .gz suffix but stayed compressed.. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "portable.h"
#include "jksql.h"
#include "cdw.h"
#include "cdwLib.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"cdwFix5 - Fix... |
78399dc2db3001a4bf42de588c4aec3578a5ad016d38b7913e1c5b614d02b5cb | C | 1,730 | 67 | /* nonCodingUi.c - char arrays for Non-Coding gene UI features */
/* Copyright (C) 2014 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "nonCodingUi.h"
#include "common.h"
/************ Biotype related controls *********/
/* T... |
b6d9efd1d4e44b82cb0c27451ee771a155511cc7c3c79016433bd05fc387752f | C | 1,730 | 50 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpcimage.h"
/*************************************************************************... |
76390988db6b93d56323e913b541e1975972bb2260376df85d76d8e3026bdfb5 | C | 1,737 | 39 | #include "cs.h"
/* C = A(p,p) where A and C are symmetric the upper part stored; pinv not p */
cs *cs_symperm (const cs *A, const int *pinv, int values)
{
int i, j, p, q, i2, j2, n, *Ap, *Ai, *Cp, *Ci, *w ;
double *Cx, *Ax ;
cs *C ;
if (!CS_CSC (A)) return (NULL) ; /* check inputs */
... |
4a10a47e99bab5e36bfd045fac94098338bd3a693ec614bc7d1b6006ecc5b6d3 | C | 1,738 | 37 | #include "cs.h"
/* sparse Cholesky update/downdate, L*L' + sigma*w*w' (sigma = +1 or -1) */
int cs_updown (cs *L, int sigma, const cs *C, const int *parent)
{
int n, p, f, j, *Lp, *Li, *Cp, *Ci ;
double *Lx, *Cx, alpha, beta = 1, delta, gamma, w1, w2, *w, beta2 = 1 ;
if (!CS_CSC (L) || !CS_CSC (C) || !paren... |
c961eba8e9acdee4a8b9509f1180fc264f8ba6ab6fefc7c1155d3eed1ed3f88c | C | 1,750 | 64 | #include "cs_mex.h"
/* A = cs_sparse2 (i,j,x), removing duplicates and numerically zero entries,
* and returning A sorted (test cs_entry) */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
CS_INT k, m, n, nz, *Ti, *Tj ;
if (nargout > 1 || nargin !... |
a1aeaf5d3bc3210369970d4bd3156f459fb5b2a4f3c7ac799fd380fdd7671621 | C | 1,751 | 78 | #include <assert.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "../../interflop_stdlib.c"
#define STR_LIM 2048
/* generate a random string of size <size> */
char *generate_string(size_t size) {
char *str = (char *)malloc(sizeof(char) * (size + 1));
for (int i = 0; i < s... |
4c235e398a2750acf759d09effbed5ff53dae203fca8638a4788f46046ebf7bb | C | 1,756 | 52 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
0c24e98af6f485dcc1cd7e9332b68a89e51b909389e6e2110e7873c035fa4d19 | C | 1,783 | 39 | #include "cs.h"
/* C = A(p,p) where A and C are symmetric the upper part stored; pinv not p */
cs *cs_symperm (const cs *A, const CS_INT *pinv, CS_INT values)
{
CS_INT i, j, p, q, i2, j2, n, *Ap, *Ai, *Cp, *Ci, *w ;
CS_ENTRY *Cx, *Ax ;
cs *C ;
if (!CS_CSC (A)) return (NULL) ; /* check... |
1336f39a26f55c0b598973c9fe9205d5725aa953ce10f0f09df2a1079889c688 | C | 1,783 | 64 | /* col gisaidSubjInfo - columns having to do with subjInfo and closely related tables. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "dystring.h"
#include "jksql.h"
#include "gisa... |
196d5ce86e2da96c3879c875d129c04aa8084a0609bceee449f8c6829dd631e9 | C | 1,783 | 52 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) YEAR OpenFOAM Foundation
\\/ ... |
61db48e5889b5b13858942c136aa3b9e0b565fd8f46133dce4691ecfd48505b2 | C | 1,788 | 52 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2014-2018 OpenFOAM Foundation
\\... |
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