sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
aabe8995c0911c78cc498f2f8308038c82433021f0154b05e23dcdbe823a33d1 | C | 1,788 | 53 | #include "cs_mex.h"
/* cs_updown: sparse Cholesky update/downdate (rank-1 or multiple rank) */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
cs Lmatrix, *Lin, Cmatrix, *C, *L, Cvector, *Cvec ;
int ignore, j, k, n, lnz, *parent, sigma = 1, cp [2] ... |
d10146868e2c3a9f11b574fdb2c0da9b5947a833d42b6df95035744eb185c093 | C | 1,788 | 52 | #include "cs_mex.h"
/* cs_symperm: symmetric permutation of a symmetric sparse matrix. */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
CS_INT ignore, n, *P, *Pinv ;
if (nargout > 1 || nargin != 2)
{
mexErrMsgTxt ("Usage: C = cs_sympe... |
7444398b4c641b4186cc5648b43459eeca3fb6f9eaecda8365fbf6c4c2f459ea | C | 1,789 | 47 | /*
* test_wide_vector_abi/test.c
*
* Vector operations wider than the target vector registers (256/512 bits on
* 128-bit NEON/SVE/SSE2), whose operands the instrumentation pass must pass to
* the MCA wrappers following the target calling convention. With the IEEE
* backend, the instrumented program must print exa... |
a9293cc951287fd347bf7d3cf86adf0920c86621a7a7d4bc542347d234ecf7c9 | C | 1,789 | 84 | /* raToCds - Extract CDS positions from ra file. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "ra.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"raToCds - Extract CDS positions from ra file\n"
"usage:\n"
" raToCds in.ra out.cds\n"
"options:\n"
" ... |
18b62ae32a9f3ac992a897723de64af5e301c526752e394adab2cb71c4a20dd7 | C | 1,791 | 68 | /* hgPal - URL entry point to library pal routines */
/* 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 "htmshell.h"
#include "cart.h"
#include "cheapcgi.h"
#include "web.h"
#include "hdb.... |
3a2098885e012f36396b4b71fbdd57ac13e9c7587419d727f53428acf219935a | C | 1,798 | 28 | /************************** SPLITMIX64 FUNCTION *******************************\
* *\
* Written in 2015 by Sebastiano Vigna ([email protected]) *\
* ... |
c40d18f2dc4b54d46b26d750aec3e9cc114e82d2208105a2408651294f46c885 | C | 1,808 | 62 | /* ========================================================================= */
/* === CAMD_control ======================================================== */
/* ========================================================================= */
/* ------------------------------------------------------------------------- */... |
887c0a18252a5365a05120d73c839a88345ec86e825cd25f6c1104d5fa741992 | C | 1,811 | 74 | /* checkableBorf - Convert borfBig orf-finder output to checkable form. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"checkableBorf - Convert borfBig orf-finder output to checkable form\n"
"usage:\n"
" checkableBorf ... |
d834642707ebe16e502bf4c0d9601f6fa6e01d18ee035161c2fd5fb97f2cc25e | C | 1,813 | 61 | /* hgBatch - Use to do batch queries of genome database over web,
* now it sends user to Table Browser which has incorporated its functions. */
/* 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"
#... |
dc7c1e15a39e1c8a36740d1b34e2a01537b052600f0f9404ca1900809eb14ce2 | C | 1,813 | 54 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
db712e64a18902bd486759a6ba06a5b0dc71bdd4b54029cf74f003ad81d39634 | C | 1,816 | 75 | /* pentCode - An in-memory structure for pentium assembly
* code, and some routines to work with it. */
#include "common.h"
#include "hash.h"
#include "isx.h"
#include "pentCode.h"
struct pentCoder *pentCoderNew(struct hash *constStringHash)
/* Make new pentCoder. */
{
struct pentCoder *coder;
AllocVar(coder);
coder... |
eb976b3de56903dbda3dc4a065ae77016a01f69ca44aaeffbda63a73cf9303d6 | C | 1,818 | 49 | #include "cs_mex.h"
/* cs_multiply: sparse matrix multiply */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
if (nargout > 1 || nargin != 2)
{
mexErrMsgTxt ("Usage: C = cs_multiply(A,B)") ;
}
if (mxIsComplex (pargin [0]) || mxIsCom... |
653a0b38a44266c282b3c2982aaddfcb23c08d8dbecea3c397c14880a02b2af9 | C | 1,821 | 50 | /* primers - do primers section. */
/* 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 "hash.h"
#include "linefile.h"
#include "dystring.h"
#include "cheapcgi.h"
#include "spDb.h"
#include... |
c35046598ac84544df54cc94c39c147ea2f11ca7daa247e9fda07909d7b30a90 | C | 1,821 | 53 | #include "cs_mex.h"
/* cs_lu: sparse LU factorization, with optional fill-reducing ordering */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
css *S ;
csn *N ;
cs Amatrix, *A, *D ;
int n, order, *p ;
double tol ;
if (nargout > 4 ||... |
ddc3f61c1561b9bba24556bd2b5374eabc6b40d0253f7bdc06bb8b81e7165446 | C | 1,821 | 78 | /* hgChroms - print chromosomes for a genome. */
/* Copyright (C) 2014 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hdb.h"
#include "options.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
... |
7d1b77c801feb21c59b6b00da743413f1009cf0e111e5fedb1d6aef72c984a01 | C | 1,825 | 70 | /* backEnd.h - interface between compiler front and back ends.
* The front end is responsible for parsing, type checking,
* and creating intermediate code. The back end is responsible
* for creating assembly language. */
#include "common.h"
#include "pfCompile.h"
#include "backEnd.h"
extern struct pfBackEnd macPe... |
5c214bc11e7a9bc45a108228030d15c5dc78d02f45275047b616d58a35245f90 | C | 1,826 | 50 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpcpar.h"
/***************************************************************************... |
bdf2faaafb1008a76c2ee11789ac059b5e50a220fff43701d0cde319894b2893 | C | 1,838 | 52 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
89ed2f4e870808620e939bcebd70f699ad295b6391433ebffcee5613d6bf0f1d | C | 1,839 | 54 | #include "cs_mex.h"
/* cs_qrsol: solve least squares or underdetermined problem */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
CS_INT k, order ;
if (nargout > 1 || nargin < 2 || nargin > 3)
{
mexErrMsgTxt ("Usage: x = cs_qrsol(A,b,o... |
318c384fa256a8dc0a05296f377f47bf7b1158daa8ed4c876093f844df6306ec | C | 1,840 | 69 | /// @file idcrypt.c
/// @author Calle Laakkonen
/// @brief Encryption/decryption of subject names and other identification
/// information in string form.
/// @note Method is simple and not safe for data transfer over internet,
/// but can be used to hide identification in blinded studies.
///
/********... |
09d5e89a2234e108402295c072a29bfe053024fd3e7c05d3f2aa4e62a4552086 | C | 1,844 | 51 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2017-2018 OpenFOAM Foundation
\\... |
26b596c78c789614e7f09f6b5cf7e3af59780562dd6a0cf782db75a3dc372614 | C | 1,847 | 56 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
84e1647acdefdf05e9536601991a3f295da548db64af61d7abc5e162c8e1c663 | C | 1,848 | 60 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
644e375d42f955bfd9553d02f53b10f40d136fae8c00b944e93014a58684fe54 | C | 1,851 | 85 | #include <values.h>
#include <stdio.h>
#include <netinet/in.h>
#include <stdlib.h>
#include <dirent.h>
#include <string.h>
#include <ctype.h>
static int *nn;
int main(int argc, char **argv)
{
int i=0,j=0,k,len=0,num_steps,nSeq,num_base;
int *s_len,BAR = 0,nstep = 0,stopflag,base;
char line[100],tempc1[100];
F... |
1190de080d10d90461f7e6ff53cb56ff6359f2fd2ac94bd1bf4d7fd24c9ea254 | C | 1,861 | 61 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2012-2018 OpenFOAM Foundation
\\... |
028245d8fec9977f19b05330b2553369b17072854708f4ac41f2d0c293e75a0e | C | 1,862 | 42 | /*
* xxHash - Extremely Fast Hash algorithm
* Copyright (C) 2012-2023 Yann Collet
*
* BSD 2-Clause License (https://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:
... |
4333d3e9c7c2aeb1774373bd791839561b6f194ede1594709dff91eafc0d898a | C | 1,862 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
1f97515143420140019609ee067f9336188cf8d79583b27f75b6c35262175559 | C | 1,863 | 56 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2014-2018 OpenFOAM Foundation
\\... |
dd114b6e8bb3016f445e0d019f2d503ba8cd407de81e4e28fd8655e251680849 | C | 1,866 | 64 | /* ========================================================================= */
/* === AMD_control ========================================================= */
/* ========================================================================= */
/* ------------------------------------------------------------------------- */... |
f749bfb217554f8247c297959513ef8b68cc6b492e87afb8e38baeb195b8e8ee | C | 1,866 | 53 | #include "cs.h"
/* x=A\b where A can be rectangular; b overwritten with solution */
int cs_qrsol (int order, const cs *A, double *b)
{
double *x ;
css *S ;
csn *N ;
cs *AT = NULL ;
int k, m, n, ok ;
if (!CS_CSC (A) || !b) return (0) ; /* check inputs */
n = A->n ;
m = A->m ;
if (m >=... |
09222deec4e532a02401640b3bce3ed33e4e716b66af7589944bb6b0af38b986 | C | 1,870 | 56 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2014-2018 OpenFOAM Foundation
\\... |
c26ec9fbb1ee9d9f5c85fe464f4350bda78bb0c959ed82bfeaa9594076035d33 | C | 1,877 | 56 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
a3530d08341db4bcf6744e4675c094ae9aef971dcc48ab2a87dbe56c05cf7ff9 | C | 1,881 | 86 | #include <values.h>
#include <stdio.h>
#include <netinet/in.h>
#include <stdlib.h>
#include <dirent.h>
#include <string.h>
#include <ctype.h>
static int *nn;
int main(int argc, char **argv)
{
int i=0,j=0,k,len=0,num_steps,nSeq,num_base;
int *s_len,BAR = 0,nstep = 0,stopflag,base;
char line[100],tempc1[100];
F... |
08c4dd9bd7abbd1175029d84295f47a15ab6d30dfc8a1afb0ce0f75fae339c56 | C | 1,882 | 57 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
5255b6f56402fbd497a6df940f2e5408103061a0cb370913c19ffe136d428eb9 | C | 1,883 | 64 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
7119f212911c18734c72276450e0ffa26bd80d1d8e43350dd3fe5c68b202f33f | C | 1,883 | 53 | #include "cs.h"
/* x=A\b where A can be rectangular; b overwritten with solution */
CS_INT cs_qrsol (CS_INT order, const cs *A, CS_ENTRY *b)
{
CS_ENTRY *x ;
css *S ;
csn *N ;
cs *AT = NULL ;
CS_INT k, m, n, ok ;
if (!CS_CSC (A) || !b) return (0) ; /* check inputs */
n = A->n ;
m = A->m ;... |
523602db4bb7f7ee85ed253d7f121a6260c1e94b1788a0df7db0ec996aadd105 | C | 1,884 | 74 | /***********************************************************************
* mexnnz.c: get number of non-zero elements of a matrix M
*
* nnz = mexnnzt(M);
*
* SDPT3: version 3.0
* Copyright (c) 1997 by
* K.C. Toh, M.J. Todd, R.H. Tutuncu
* Last Modified: 2 Feb 01
*******************************************************... |
c3a8ed25e197a750d4448742eccf7f98824597173f3392c2443395df02705c20 | C | 1,886 | 41 | #include "cs.h"
/* find the strongly connected components of a square matrix */
csd *cs_scc (cs *A) /* matrix A temporarily modified, then restored */
{
int n, i, k, b, nb = 0, top, *xi, *pstack, *p, *r, *Ap, *ATp, *rcopy, *Blk ;
cs *AT ;
csd *D ;
if (!CS_CSC (A)) return (NULL) ; /* c... |
1bca75f94a7d05e397e684e247e144bf8dd8a18977bfc8279684ee11c0553f9e | C | 1,887 | 57 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
ebe99a5fa1583c4a2fe34341c8f8ec4d52427d41dbf279a1f1cbb005d32f6f6d | C | 1,887 | 73 | #include<pandaseq-plugin.h>
#include<math.h>
HELP("Remove reads with another primer. Use f for forward, r for reverse.", "other_primer:[fr]:NNNNN");
VER_INFO("1.0");
struct data {
size_t primer_length;
bool forward;
panda_nt primer[1];
};
static bool precheck_func(
PandaLogProxy logger,
const panda_seq_identif... |
10942af2b7d5ebc1f13d857f849efe4071258b24d1f300749e3e901db81a74b7 | C | 1,889 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2013-2018 OpenFOAM Foundation
\\... |
7af9aed12343fe72b868ef4e718cae82d2789a6fb3fb2604baefdb881776cdaa | C | 1,892 | 41 | #include "cs.h"
/* find the strongly connected components of a square matrix */
csd *cs_scc (cs *A) /* matrix A temporarily modified, then restored */
{
CS_INT n, i, k, b, nb = 0, top, *xi, *pstack, *p, *r, *Ap, *ATp, *rcopy, *Blk ;
cs *AT ;
csd *D ;
if (!CS_CSC (A)) return (NULL) ; /... |
d24df4fb37e57b9db040cbdd8fbbabeb7871e1e364ee04b6f505cf1500939628 | C | 1,895 | 44 | /* PANDAseq -- Assemble paired FASTQ Illumina reads and strip the region between amplification primers.
Copyright (C) 2014 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 Foundati... |
d298b554b820c5815d0575f982713812e690b728fd8627762f647128f3e3f7c8 | C | 1,895 | 81 | /*
* 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... |
6366f5793ee912d1b8e6a6911a3d0a25616c25eb4b433a630ce4cbd187efe966 | C | 1,897 | 63 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
e6989d8fbea30f47439f1cf0e4b5b17456f6acc9efc5c2f2a6f2133d6bbf11d6 | C | 1,904 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
8ed7ad311f111075c58182cf6aed3d3bcda0b25c0da760adb96356132006594a | C | 1,905 | 61 | #include "cs_mex.h"
/* cs_lusol: solve A*x=b using a sparse LU factorization */
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double tol ;
CS_INT order ;
if (nargout > 1 || nargin < 2 || nargin > 4)
{
mexErrMsgTxt ("Usage: x = cs_... |
cde9d62e0ec9538b88f5fb81cf736b48bd6a90a1529c35aeb67a132fee00b24f | C | 1,909 | 61 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
c80df3f18b9675b1195ecdc9a22f6bf187b0b353115c6faef1d8ede369d8e001 | C | 1,910 | 68 | #include "fpPropImpl.c"
#include <assert.h>
#include <math.h>
int main(int argc, char** argv){
if(!((argc==3)|| (argc==4) )){
printf("usage ./propFP range precision [value]\n");
printf("\tfor float ./propFP 8 23\n");
printf("\tfor double ./propFP 11 52\n");
return EXIT_FAILURE;
}
in... |
d6674f56fcde79e8eb04fbad1d63e8d998f19e0e19af8e819b8b69b8da577d25 | C | 1,913 | 84 | /* tagToBed12 - Convert tagAlign format to bed 12 + 2. */
/* 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 "bed12wSeq.h"
#incl... |
2151a3f969be411543d41985b1617d0602b000b21a5d539a0629221e40c2f5b3 | C | 1,914 | 62 | /* edwRunOnIds - Run a edw command line program (one that takes startId endId as it's two parameters) for a range of ids, putting it on edwJob queue.. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "com... |
bc4c6829e6cf52402a14cf513f3b99fe271cd056c03e0b0749d15b096dfc7271 | C | 1,914 | 67 | #include "cs_mex.h"
/* find nonzero pattern of x=L\sparse(b). L must be sparse, real, and lower
* triangular. b must be a real sparse vector. */
static
void dfsr (int j, const cs *L, int *top, int *xi, int *w)
{
int p ;
w [j] = 1 ; /* mark node j */
for (p = L->p [j] ; p ... |
ce9a9bbbf23066a65de3350fdaece975a586321d6db565a2eec434d87b3985b5 | C | 1,915 | 55 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
6f5929bf11bf3a13a4fad58c19ed493cb52c974188aad0cd19d852826cde41c8 | C | 1,920 | 54 | /** @file parorder.c
* @brief Sort or otherwise change the order of data in PAR struct.
*/
/*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include <stdio.h>
#include <std... |
688c8461dd426419b48aee46deb53bc5f2e7d3c7c80cce6a67687334517dcaf0 | C | 1,922 | 120 |
#include "common.h"
#include "cart.h"
static char *edit0Mm10tracks[] =
{
"snp142",
"snp142Mult",
"snp138",
"snp138Common",
"snp138Mult",
"snp137Common",
"snp137Mult",
"snp137",
};
static char *edit0Hg19tracks[] =
{
"snp151Flagged",
"snp151Mult",
"snp150Mult",
"snp150Flagged",
"snp150",
"snp150Common",
"snp149Mult",
... |
485d86b8f8b8856dd3c8ef6a082254c6a4e99b65a42c9c27a724e6efe5c56785 | C | 1,924 | 66 | /// @file mestim.c
/// @author Kaisa Sederholm, Vesa Oikonen
/// @brief Calculating Hubers M-estimator for single data.
///
/*****************************************************************************/
#include "libtpcmodel.h"
/*****************************************************************************/
/*********... |
49bf887a5b2549f24beef8ebf7ff2e1bb1bc4106536281fe569590de4bb4b863 | C | 1,925 | 71 | /* eapAddSoftware - Add a new software object. */
/* Copyright (C) 2014 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 "../../encodeDataWarehouse/... |
f8fbf6f93de65f68caa783b0d175be86f74f1bd23eaed60a3164518c17b73c01 | C | 1,925 | 61 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
ba0706d7d9deec71ccb2cbfb886314f387227895378c695c56c150f5728fb995 | C | 1,929 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
aa09a031983685060d56d8346da8ee8c981ae181842152523f3f9bd3dc9502c7 | C | 1,930 | 57 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2014-2018 OpenFOAM Foundation
\\... |
3cbfa3798aa422708d1de1f82b4a6a61856f229a8a897036401d632fa1cafcda | C | 1,932 | 68 | /*****************************************************************************\
* *\
* This file is part of the Verificarlo project, *\
* under the Apache License v2.0 with LLVM Exceptions. *\
... |
4bfe89830a6ca64415244ed87078588d8114dd88fc55d7a9dba555665fa1fc9f | C | 1,932 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
50f92351a2e75d7aca30d1822d3edb5e3ce7548faac34be5a88ee60aab7c63bc | C | 1,932 | 58 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
d1fecbc32340b84073aed49aaa9755bdcbf1f4adc629224e002829dd473f50d1 | C | 1,933 | 62 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
905e229838a7245be00d2f91d0a5e42cac2e7137fab901226396d17aca3be50c | C | 1,934 | 61 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
67f135610542b10b4e0933fb8e9a732d661c4b6be551536e61b8bc9705fb7a8c | C | 1,938 | 59 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2015-2018 OpenFOAM Foundation
\\... |
ac26288821fb3a0e7d4e3aebdac1b364fcbba81d0d2704d65af91dfcf5f64251 | C | 1,940 | 84 | /* hgNotAvail - Human 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 "linefile.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "obscure.h"
#... |
2dff0d99f03420fb6f4bd74e36f69792f2fa9fbe39d8e5c649454dbfe3d560d6 | C | 1,947 | 67 | #include "cs_mex.h"
/* find nonzero pattern of x=L\sparse(b). L must be sparse and lower
* triangular. b must be a sparse vector. */
static
void dfsr (CS_INT j, const cs *L, CS_INT *top, CS_INT *xi, CS_INT *w)
{
CS_INT p ;
w [j] = 1 ; /* mark node j */
for (p = L->p [j] ;... |
bacbf43fc81576da4ea4df9ecf39b2e11a9f3c1d30f562407c58242c7885ba47 | C | 1,947 | 81 | /* hgsqlSwapTables - swaps tables in database. */
/* 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 "jksql.h"
#include "hdb.h"
... |
f656c1c7a3141625f7e1a3dc403a633a994b2e6e8d9c906e5a1e12b1ef08341b | C | 1,949 | 53 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpccm.h"
/****************************************************************************... |
ddd05bb0f0e2980663e6da36778e9235bb9f25ee405752ba062c8a1dbde6861b | C | 1,951 | 73 | /*
* 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... |
a7d40cb580dcc4be5fe271c48996e309f342425d59efd4414fd9d831454a5a0f | C | 1,952 | 65 | #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
... |
9f0230c7c8f110729710ac75a813d1cc9a620631c65d6d2014be11b09ea8419d | C | 1,953 | 53 | /*****************************************************************************/
#include "tpcclibConfig.h"
/*****************************************************************************/
#include "tpcextensions.h"
#include "test_tpccm.h"
/****************************************************************************... |
2c0009c4f2b34305a2d492a1d8892646bf7cb9d7058a87c3a913fd3ecbbb8b40 | C | 1,959 | 66 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
85addac77e427c888a59866273641c8b30a36cbd26ae3a1ed557f7af2984fbf9 | C | 1,963 | 92 | #define _GNU_SOURCE
#include <math.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#ifndef N
#define N 100
#endif
#define xstr(X) str(X)
#define str(X) #X
#ifndef REAL
#error "Type is not defined"
#endif
#ifndef FUNCTION
#error "Function to evaluate is not defined"
#endif
#ifdef PROFILING
#ifdef __i3... |
a3d54eaae076e19412bf0ac14622f9b1f21cba000e01bb61d4b846f4e540aa0a | C | 1,969 | 77 | #include "common.h"
#include "jksql.h"
#include "linefile.h"
#include "ra.h"
#include "trackDb.h"
#include "assoc.h"
char *getAssoc(struct sqlConnection *conn, char *table, char *field, char *whereField, char *whereValue)
{
char query[4096];
char result[4096];
sqlSafef(query, sizeof query, "select %s from %s where ... |
60ce209e195d9eca2e8a353526d784d646d3c25a16a9a0f0bacf4e6fe4f28b6e | C | 1,977 | 68 | /* cdwSwapInSymLink - Replace submission file with a symlink to file in warehouse.. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "jksql.h"
#include "cdw.h"
#include "cdwLib.h"
#include "portable.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"cdwSwapInSymLin... |
ca60b46cae91a5078b39571ca677b20706d4f1462b3c9bc756da2db858537219 | C | 1,977 | 46 | /* 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... |
0f004ae895fcbea13f7812c4689f37ee04fdace1be8aa3278fbb4017574ed238 | C | 1,982 | 74 | /* cdwUnlockSubmittedFile - unlock a symlink to a read only submitted file, returns it to a normal file.
* This utility can be run from either the wrangle/ or submit/ directories. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "filePath.h"
#include "dystring.h"
#include... |
6a3bda2b120e4f6377ddfa6014fe62c6a5009885b5a92589c847dfa40ce2b3af | C | 1,984 | 65 | /* edwFixBasesInSample - Fill in basesInSample field for fastqs from edwValidFile.. */
/* 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"... |
de6b7f11c633455e4821086804cc0e0f03371201f475e2dc25c175719386de4f | C | 1,987 | 67 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
747defe5142c923431b69c357e18b312834705a41b9843e12cae4b478c5e2037 | C | 1,988 | 62 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
27a7f6937b4d6387838e2fa050162c08c71f6531083d269855e4295b16aa5c93 | C | 1,989 | 59 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2015-2018 OpenFOAM Foundation
\\... |
37ba7c8d167de40ae083b295ebabdde1783d47c491b6f131acc345b29d79b596 | C | 1,989 | 51 | /* ========================================================================= */
/* === CAMD_postorder ====================================================== */
/* ========================================================================= */
/* ------------------------------------------------------------------------- */... |
692ef49584ddc21330a7b624132e11a758453bd48c427bea69934f0427dfa43f | C | 1,992 | 71 | /* ========================================================================== */
/* === KLU_free_numeric ===================================================== */
/* ========================================================================== */
/* Free the KLU Numeric object. */
#include "klu_internal.h"
Int KLU_free_... |
6aedcdce524c24db4c935c17fc1b0903cf85cf974d83a9f00672e1228e1cc889 | C | 2,011 | 60 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
8bfb6787e9a5809d5de246d7b6e6b622dfcb6d144cdc7be15f7074678c26604b | C | 2,013 | 57 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2013-2018 OpenFOAM Foundation
\\... |
070921461107e54de087b34bfff2b8e0d03cd3bb786fa9b126b92a84d83f716e | C | 2,015 | 83 | /* hgNotYet - Human 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 "linefile.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "obscure.h"
#in... |
8e45a24aa805143a2755693388b6826b2586e033f86d2381644573030b6fe57a | C | 2,019 | 60 | /* mouseOver.c
* Some routines for managing the mouseOver options for bigBed-like tracks, where mouseover can
* optionally be drawn from any (or any combination) of fields.
*/
// arguably these routines should go in bigBedTrack.c
#include "common.h"
#include "cart.h"
#include "trackDb.h"
#include "hgTracks.h"
#inc... |
67a31c69cf53fdeb80650f5be36ea7827bf7d13534274f8385aaf8d1822bb131 | C | 2,020 | 85 | /* pairedTagToBed12 - Convert pairedTagAlign format to bed 12 + 2. */
/* 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 "bed12w... |
9ca485a00ee46e31a0ea1d92c1aa913d8e35f1e050d26689eaa06302d03917e5 | C | 2,022 | 64 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation
\\... |
a922fd0160353ec83abe0c43ed7a686f9b4be0788d0374d205c00349b6ab95b3 | C | 2,022 | 65 | /* lrgTrack.c - display Locus Reference Genomic (LRG) sequences mapped to genome assembly */
/* 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 "hgTracks.h"
#include "bigBed.h"
#include "lr... |
5e0a41661e297ed1ef4da69f938b6c7a374479bd752cbe39a857c8aae257493f | C | 2,026 | 78 | /* edwSolexaToSangerFastq - Subtract 31 from each quality to get from solexe to sanger format.. */
/* Copyright (C) 2014 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... |
7675e4933ae20a29864bc4009b52ba94d4b9dad1752f13d45a402fb81b386044 | C | 2,028 | 75 | /*
* 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... |
9bc35f620783d5989f373fe1ad7a551df2f8e73b66683db6f08fa560e8f3bea0 | C | 2,028 | 102 | /* Y=spktime2count(s,idx, Tw, Ncount,option) */
/* Y is neuron # by trial #
counts are non-overlapping
option=1, if neuronIdx is continuous and sorted, 0 if not
*/
/*neuruon IDs */
#include "mex.h"
#include "math.h"
#include "time.h"
#include "matrix.h"
void mexFunction(int nlhs, mxArray *plhs[], int n... |
11481e3a62c76e8e3e05580dee685554865b1678a3b6f61b78aeb9a5980720ba | C | 2,034 | 60 |
// 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"
#... |
d55bde62e63cfcad6bf1c4678ab7bdf3635f5ce3ad0b5e10efc6a259094c26d3 | C | 2,038 | 70 | /***********************************************************************
* mexexpand.c : C mex file
*
* z = mexexpand(blk,x);
*
* Input: blk = [n1, n2, ..., nk]
*
* Output: [x1 x1...x1, x2 x2...x2, ...., xk xk...xk]'
* n1 n2 nk
*
* SDPT3: version 3.0
* Copyr... |
d9f9e34812b12143bc284dc23c6601581ebdf5171a5ee2bda4d07d52f2f7c9c4 | C | 2,038 | 100 | #include "config.h"
#include <bzlib.h>
#include <stdlib.h>
#include "pandaseq.h"
#include "misc.h"
struct bz_stream_data {
bz_stream strm;
size_t buffer_length;
MANAGED_MEMBER(
PandaBufferRead,
source);
char buffer[];
};
static bool read_stream(
char *buffer,
size_t buffer_length,
size_t *read,
struct bz... |
ad3675499729bf099e99c149fe57721526208fce631680a2e8738c81807305b7 | C | 2,044 | 65 | /*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation
\\... |
07a7a8111c0c44364f5840aaf08f340bab49e822e69a4ca503f27701504444e7 | C | 2,045 | 78 | /* cirmTags - A program that may eventually handle the .xlxs format (Excel), and parse tags. Rough draft for now. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "common.h"
#include "options.h"
#include "cdwValid.h"
#include "tokenizer.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
... |
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