sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7e0242158481e0968aa77b713ea970ac4f345ecfa5e905925677e7a60b79df59 | C | 10,300 | 347 | /**
Copyright (C) powturbo 2013-2018
GPL v2 License
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, or
(at your option) any later version.
... |
9abd3d3b4a635c8a2768ffcc51a4c78c7bc34bdf13e518576bd0a6019eef5565 | C | 10,467 | 305 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
456c8e0b6c6af147cf827debf80ba0c1a1870b9543713e2d380a6b9fd94dae77 | C | 10,529 | 418 | #include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "../linear.h"
#include "mex.h"
#include "linear_model_matlab.h"
#ifdef MX_API_VER
#if MX_API_VER < 0x07030000
typedef int mwIndex;
#endif
#endif
#define CMD_LEN 2048
#define Malloc(type,n) (type *)malloc((n)*size... |
a77fba0a3e7aaec2e805f6c19e5a56c7678f40671ce6bfba55850129eeea5ab2 | C | 10,683 | 272 | /*
L = symfctmex(X, perm)
Computes sparse symbolic factor L.L, updated permutation L.perm,
super-node partition L.xsuper.
Invokes SPARSPAK-A (ANSI FORTRAN) RELEASE III,
by Joseph Liu (UNIVERSITY OF WATERLOO).
*/
/*
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 ... |
d28f3109cee85870bb29d48d487c3460cb7f75f2bb5de91da443dcfba5f87bee | C | 10,753 | 421 | #include "config.h"
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include "htslib/bgzf.h"
#include "htslib/faidx.h"
#include "htslib/khash.h"
#ifdef _USE_KNETFILE
#include "htslib/knetfile.h"
#endif
typedef struct {
int32_t line_len, line_blen;
int64_t len;
uin... |
4ba56283bc86b8e29cbcabb81292b7a7ddb919ef0d6441ef85c4df1b324e79f0 | C | 10,836 | 311 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
5f449051460fda5b392670dc0f6724f2b8f8ef9236d888ac717f959311839271 | C | 11,015 | 386 | /*
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,
... |
776fd918818d0699f36e3ddc847c7df6f890bc131bc4b9f895e8375c3223ecc9 | C | 11,069 | 244 | /*
% Ad = Adendotd(dense, d, sparAd, Ablk, blkstart)
% ADENDOTD Computes d[k]'*Aj[k] for Lorentz blocks that are to be factored
% by dpr1fact.
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function Ad = Adendotd(dense, d, sparAd, Ablk, blkstart)
% This file is pa... |
09ec25e82cb7bf79325030e1896820bea23f5098a7380a1675b8b83eb2d3bb46 | C | 11,180 | 341 | /***********************************************************************
* mexmat.c : C mex file
*
* M = mexmat(blk,x,isspM,rowidx,colidx,iscellM);
*
* SDPT3: version 3.0
* Copyright (c) 1997 by
* K.C. Toh, M.J. Todd, R.H. Tutuncu
* Last Modified: 2 Feb 01
************************************************************... |
bf31504ddafa2a62e12a611918164821eabad1aa31d0939daf2587febd653a89 | C | 11,249 | 275 | /*
% y = bwdpr1(Lden, b)
% BWDPR1 Solves "PROD_k L(pk,betak)' * y = b", where
% L(p,beta) = eye(n) + tril(p*beta',-1).
%
% SEE ALSO sedumi, dpr1fact, fwdpr1
% ********** INTERNAL FUNCTION OF SEDUMI **********
function y = bwdpr1(Lden, b)
% This file is p... |
a24cc0aa5338e7298617f914865248ca46c407e9b24035779eb2c8bd03fd1bcf | C | 11,492 | 296 | /*
[q,r] = qrK(x,K);
* x should consist only of SDP part (length sum(K.s.^2)).
* q is in product form: the n-1 factors are:
I- q(k:n,k)*q(k:n,k)' / beta(k).
For real PSD blocks, beta[k] = q(k,n)
For complex PSD blocks, beta[k] = q(k,2*n+1), and q is n * (2n+1).
* tril(r) will be all-0.
qrK: Q(bet... |
19b22c9a446fd63b22e7e69b68ac69c6dcde52377f16b0594a9a13429d2f0eef | C | 11,836 | 261 | /* ************************************************************
% ADA = getada1(ADA, A,Ajc2,perm, d, blkstart)
% GETADA1 Compute ADA(i,j) = (D(d^2; LP,Lorentz)*A.t(:,i))' *A.t(:,j),
% and exploit sparsity as much as possible.
% Ajc2 points just beyond LP/Lorentz nonzeros for each co... |
ea8995eb7dd9ee1b7b4d77b60da0ad9d14381e804a1565cc90f96b61f297044f | C | 12,060 | 397 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu)
// This file is part of MMLDA-C.
// MMLDA-C 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, or (at your
// option) any... |
095e2e1563ff79561590ccce5c934d15168499b8cb5b640c2fbf40e933a56489 | C | 12,222 | 473 | /*
* ==============================================================
* max_flow_mex.c The mex interface to the matlab bgl wrapper.
*
* David Gleich
* 16 April 2006
* =============================================================
*/
/*
* 15 June 2006
* Changed error message.
*
* 19 February 2007
* Updated to... |
a8ddd7f2e9f4e6965d8212f2bf587ed37c012e5dcf00332f5fd3377b81d4d79a | C | 12,224 | 432 | /*
Author: James Bonfield (jkb@sanger.ac.uk)
Copyright (c) 1995-1996 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 c... |
e01b3d4475d207dda1538e79202a138ef3905a6a246cf289f363e57608f370bf | C | 12,224 | 298 | /*
y = bwblkslv(L,b, [y])
Given block sparse Cholesky structure L, as generated by
SPARCHOL, this solves the equation "L.L' * y(L.perm) = b",
i.e. y(L.perm) = L.L'\b. The diagonal of L.L is taken to
be all-1, i.e. it uses eye(n) + tril(L.L,-1).
CAUTION: If y and b are SPARSE, then L.perm is NOT us... |
ab8c0054398c78b5b5834d12aceba66f18bec2823ac88bbe6390759bdf9b364f | C | 12,305 | 460 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
72ebd8c444c65326dc5c637586c34977999037e58714712c74e6a6fe7f9257e1 | C | 12,599 | 503 | /*
Copyright (c) 2013-2014 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this l... |
df07d76a0bf44b6fc87ea0618bbf3e38209cb656c14573673cd1fcff0492a93c | C | 12,695 | 320 | /*
y = fwblkslv(L,b, [y])
Given block sparse Cholesky structure L, as generated by
SPARCHOL, this solves the equation "L.L * y = b(L.perm,:)",
i.e. y = L.L\b(L.perm,:). The diagonal of L.L is taken to
be all-1, i.e. it uses eye(n) + tril(L.L,-1).
If b is SPARSE, then the 3rd argument (y) must give... |
4d496ab2a3d29df5fadc3dbff6067e039806aaceae6cfcd09ea77d46c2b848fd | C | 12,978 | 323 | /* inffast.c -- fast decoding
* Copyright (C) 1995-2017 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "zutil.h"
#include "inftrees.h"
#include "inflate.h"
#include "inffast.h"
#ifdef ASMINF
# pragma message("Assembler code may have bugs -- use at your own risk")
#... |
1960ca67384376f65b6ce8c08fdb501f8eb33923e11ef5f61a855708c6cb0a8a | C | 12,999 | 304 | /* inftrees.c -- generate Huffman trees for efficient decoding
* Copyright (C) 1995-2017 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "zutil.h"
#include "inftrees.h"
#define MAXBITS 15
const char inflate_copyright[] =
" inflate 1.2.11 Copyright 1995-2017 Mark ... |
21150f590e1c11182b709517fd00f2183338807d84cf92140bac3bf269039c80 | C | 13,112 | 462 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu)
// This file is part of MMLDA-C.
// MMLDA-C 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, or (at your
// option) any... |
129983f2807b1ac738208edf2812912d5a99d0baab6c2a92763629a65ebe2886 | C | 13,280 | 308 | /*
% ddotX = ddot(d,X,blkstart [, Xblkjc])
% DDOT Given N x m matrix X, creates (blkstart(end)-blkstart(1)) x m matrix
% ddotX, having entries d[i]'* xj[i] for each (Lorentz norm bound) block
% blkstart(i):blkstart(i+1)-1. If X is sparse, then Xblkjc(:,2:3) should
% point to first ... |
22565252fbf98da8282fea5cdd31cff23851ba2182434eb577757d04d9bc4cbb | C | 13,325 | 374 | #include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <getopt.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <errno.h>
#include "htslib/tbx.h"
#include "htslib/sam.h"
#include "htslib/vcf.h"
#include "htslib/kseq.h"
#include "htslib/bgzf.h"
#include "htslib/hts.h"
typedef st... |
0c7f10396703b230c504207fe1595a2f2f8ba9c43158c4bd79d5b22ca36e04e0 | C | 13,406 | 324 | /* inftree9.c -- generate Huffman trees for efficient decoding
* Copyright (C) 1995-2017 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "zutil.h"
#include "inftree9.h"
#define MAXBITS 15
const char inflate9_copyright[] =
" inflate9 1.2.11 Copyright 1995-2017 Mar... |
a04af273e83ecc351bf3794974ab2098d8d960df4044b7b44734c41443ee26d0 | C | 14,053 | 442 | /* crc32.c -- compute the CRC-32 of a data stream
* Copyright (C) 1995-2006, 2010, 2011, 2012, 2016 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*
* Thanks to Rodney Brown <rbrown64@csc.com.au> for his contribution of faster
* CRC methods: exclusive-oring 32 bits of data at a... |
90b9d6c39a5fc91cf1cc9b96b025a508a8015dc502cd9374c754b44078593f57 | C | 14,132 | 449 | /* gzjoin -- command to join gzip files into one gzip file
Copyright (C) 2004, 2005, 2012 Mark Adler, all rights reserved
version 1.2, 14 Aug 2012
This software is provided 'as-is', without any express or implied
warranty. In no event will the author be held liable for any damages
arising from the use of t... |
2c05bc374d3d847c6a9f29eac9d674abba7659d1e91e34e172248fcb5c274d51 | C | 14,223 | 462 | /* iowin32.c -- IO base function header for compress/uncompress .zip
Version 1.1, February 14h, 2010
part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modification... |
f235267649b1fae420ec58b93ea59e474dcfdfc311de39316be09c630c00a27a | C | 14,445 | 526 | /* hfile.c -- buffered 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
in the Soft... |
3de4f0cbe3bd7624c06a4a263771e455d1524942b390140b98199d14504fda96 | C | 14,521 | 446 | #include <assert.h>
#include <errno.h>
#include <string.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdlib.h>
#include "htslib/sam.h"
#include "kvec.h"
#include "kstring.h"
#include "medaka_trimbam.h"
#include "medaka_bamiter.h"
#include "medaka_common.h"
#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4... |
5f584a5bea62af468b3f4434f87605c1d47a909ba0a3580988a551d745e9bd29 | C | 14,719 | 372 | #define _GNU_SOURCE
#include <assert.h>
#include <errno.h>
#include <math.h>
#include <string.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include "htslib/sam.h"
#include "khash.h"
#include "kvec.h"
#include "medaka_bamiter.h"
#include "medaka_common.h"
#include "medaka_counts.h"... |
bc756f86719228c647afbc4b19edf73c66d57ec7d896f34944eeebc8ef4d5934 | C | 14,770 | 343 | /* ************************************************************
% [perm, dz] = incorder(At [,Ajc1,ifirst])
% INCORDER
% perm sorts the columns of At greedily, by iteratively picking
% the 1st unprocessed column with the least number of nonzero
% subscripts THAT ARE NOT YET COVERED (hence ... |
63880edc71f183e117ad7e0a8d1ef58850f6afa5f6f33f516c1fe82eda3b17a7 | C | 14,803 | 357 | /*
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept. Econometrics & O.R., Tilburg University, the Netherlands.
% Supported by the Netherlands Organization for Scient... |
35c3bc6fd7b8a9b9211cccbd450c0b095c157115a76f1ec87aeafa55e804af15 | C | 14,889 | 454 | /***********************************************************************
* mexsmat.c : C mex file
*
* M = mexsmat(blk,x,isspM,rowidx,colidx,iscellM);
*
* SDPT3: version 3.0
* Copyright (c) 1997 by
* K.C. Toh, M.J. Todd, R.H. Tutuncu
* Last Modified: 2 Feb 01
*******************************************************... |
fdfcf83979ef2324c1455d369e8add8678c804939d412ce53f8b024578ceabad | C | 15,034 | 520 | /*
minizip.c
Version 1.1, February 14h, 2010
sample part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modifications of Unzip for Zip64
Copyright (C) 2007-2... |
840ebeb058cd0ca9e92dcb1db665932462a4695fc649b34e865b8d1ad7c5bf77 | C | 15,438 | 409 | /* zran.c -- example of zlib/gzip stream indexing and random access
* Copyright (C) 2005, 2012 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
Version 1.1 29 Sep 2012 Mark Adler */
/* Version History:
1.0 29 May 2005 First version
1.1 29 Sep 2012 Fix memory reallocation... |
9a5264a3b538e3e19d4d15721fce3b2e9f288576d4e0c7d939b5df9aee92a39a | C | 15,686 | 634 | /*
Copyright (c) 2005-2006, 2008-2009, 2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyrigh... |
91089b21e692797bb6208b2b45eeb90f5f1f1e4f6b67b99dea5676f51b811193 | C | 15,797 | 651 | /* minigzip.c -- simulate gzip using the zlib compression library
* Copyright (C) 1995-2006, 2010, 2011, 2016 Jean-loup Gailly
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/*
* minigzip is a minimal implementation of the gzip utility. This is
* only an example of using zlib and isn'... |
d39498b0bcf613a92bfa799f6ae9de9a33e88e3a9fb301f5e2563ff9aba65f9b | C | 16,214 | 377 | /*
x = symbfwblk(L, b)
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept. Econometrics & O.R., Tilburg University, the Netherlands.
% Supported by the Netherlands O... |
9ac9938630b94becfdfadf1e556f01975bdf93439d4a846750b5bb5a49b57c0d | C | 16,363 | 713 | /*
Copyright (c) 2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list o... |
42f328e354e63b0b71bd58220c6d9977bed276d05571b58afb39c8646169fdbf | C | 16,436 | 471 | /*****************************************************************************
* mexschur.c : C mex file to compute
*
* mexschur(blk,Avec,nzlistA1,nzlistA2,permA,U,V,colend,type,schur);
*
* schur(I,J) = schur(I,J) + Trace(Ai U Aj V),
* where I = permA[i], J = permA[j], 1<=i,j<=colend.
*
* i... |
9a12d774301d252dcd38bba07ac369319da4c04c4fef8a50fcbf40aebf29c2a1 | C | 16,542 | 674 | /*
* untgz.c -- Display contents and extract files from a gzip'd TAR file
*
* written by Pedro A. Aranda Gutierrez <paag@tid.es>
* adaptation to Unix by Jean-loup Gailly <jloup@gzip.org>
* various fixes by Cosmin Truta <cosmint@cs.ubbcluj.ro>
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include... |
5daf11e44149e0aba2956d35f73f04f35dca99c3dfa43f5ad43ec20b336e4a1b | C | 16,599 | 637 | /* gzlib.c -- zlib functions common to reading and writing gzip files
* Copyright (C) 2004-2017 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "gzguts.h"
#if defined(_WIN32) && !defined(__BORLANDC__) && !defined(__MINGW32__)
# define LSEEK _lseeki64
#else
#if defin... |
e91b6ccd89ce4aecd30c75051f3721e1cd551cac46656f67bdc3c0cb3c2cf362 | C | 16,886 | 657 | /*
* $Id: file2mat.c 6618 2015-12-01 16:25:38Z spm $
* John Ashburner
*/
/*
Memory mapping is used by this module. For more information on this, see:
http://www.mathworks.com/company/newsletters/digest/mar04/memory_map.html
*/
#define _FILE_OFFSET_BITS 64
#include <math.h>
#include <fcntl.h>
#include <sys/stat.h>... |
520799662a8286725540d6d5a356efe6f595618e5fe2e591972491d719bd99aa | C | 16,888 | 602 | /* example.c -- usage example of the zlib compression library
* Copyright (C) 1995-2006, 2011, 2016 Jean-loup Gailly
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/* @(#) $Id$ */
#include "zlib.h"
#include <stdio.h>
#ifdef STDC
# include <string.h>
# include <stdlib.h>
#endif
#if ... |
55f3bb14d7fabe8ba85dc027bbfa3c7bfdd84dfb3ee76a811f90bba3331c12d5 | C | 16,914 | 708 | /*
* Copyright 1996-2006 Catherine Loader.
*/
#include "mex.h"
/*
* Copyright 1996-2006 Catherine Loader.
*/
/*
* Copyright (c) 1998-2006 Catherine Loader.
* This file contains functions to compute the constants
* appearing in the tube formula.
*/
#include <stdio.h>
#include <math.h>
#include "tube.h"
... |
4182d38bf97ffbdf1110df7f65c0e8fab0b28b1ea36ebba8621c14e8e76f1caa | C | 16,977 | 504 | /* gzappend -- command to append to a gzip file
Copyright (C) 2003, 2012 Mark Adler, all rights reserved
version 1.2, 11 Oct 2012
This software is provided 'as-is', without any express or implied
warranty. In no event will the author be held liable for any damages
arising from the use of this software.
... |
ced49f20c62536a8ffb270b35cfa4994a1dcdce45f8cf059b941c94ca0022666 | C | 17,763 | 660 | /*
miniunz.c
Version 1.1, February 14h, 2010
sample part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modifications of Unzip for Zip64
Copyright (C) 2007-2... |
7132d1c72840fe67e2b773c3f3d3cf4dfe82a1e3819dd392b2a54bcd583cfb7b | C | 18,060 | 522 | /**
Copyright (C) powturbo 2013-2018
GPL v2 License
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, or
(at your option) any later version.
... |
1ab3e479d342bfc144167b808fb00142264bc50f24a110ca88cc774e351c218e | C | 18,162 | 466 | /* blast.c
* Copyright (C) 2003, 2012, 2013 Mark Adler
* For conditions of distribution and use, see copyright notice in blast.h
* version 1.3, 24 Aug 2013
*
* blast.c decompresses data compressed by the PKWare Compression Library.
* This function provides functionality similar to the explode() function of
* the... |
f7e7248d31751700c4314dc983fd8cb535ce6adad7b20d57903487f13d6b0778 | C | 18,309 | 622 | /* The MIT License
Copyright (c) 2008 by Genome Research Ltd (GRL).
2010 by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software wi... |
15aa5cc9568b7591e830ca64204512657958e820dc03fc5e32aeaadaee7a3600 | C | 19,165 | 440 | /*
% [L.L, L.d, skip, diagadd] = blkchol(L,ADA [,pars [,absd]])
% BLKCHOL Computes sparse lower-triangular Cholesky factor L,
% L*L' = P(perm,perm)
% Input Parameter L is typically generated by symbchol.
% Parameters: pars.canceltol and pars.maxu.
% Optional: absd to force adding diag if drop... |
ba3b7b7ad2ff7ef0c19319b8408c333491a4cd495da55d0b156bc73d9ddb4df4 | C | 19,253 | 665 | /* gzwrite.c -- zlib functions for writing gzip files
* Copyright (C) 2004-2017 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "gzguts.h"
/* Local functions */
local int gz_init OF((gz_statep));
local int gz_comp OF((gz_statep, int));
local int gz_zero OF((gz_statep... |
6f928512cb1792cfeab31a51ff0b211814d2e455bc75290eb31079dc1e5ad2ec | C | 20,428 | 654 | /* gzread.c -- zlib functions for reading gzip files
* Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013, 2016 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "gzguts.h"
/* Local functions */
local int gz_load OF((gz_statep, unsigned char *, unsigned, unsigned *));
lo... |
442b131845c16504a3a5ce3c57b9c33bc3029c85a15a69a53bfa1c1b77c8223c | C | 20,461 | 488 | /*
% [u,perm,gjc,g] = urotorder(u,K, maxu,permIN)
% UROTORDER Stable reORDERing of triu U-factor by Givens ROTations.
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function [u,perm,gjc,g] = urotorder(u,K, maxu,permIN)
% This file is part of SeDuMi 1.1 by Imre Polik a... |
0a715c85a1ce3bb8b5a18d60941ffabc0186a886bcc66ba2ee0c4115a8e274e9 | C | 21,629 | 615 | /* infback9.c -- inflate deflate64 data using a call-back interface
* Copyright (C) 1995-2008 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "zutil.h"
#include "infback9.h"
#include "inftree9.h"
#include "inflate9.h"
#define WSIZE 65536UL
/*
strm provides memory... |
b6ceeabef3a87e0f7d193752b7380961e94ee6111d1695ac279acdc422556406 | C | 22,328 | 466 | /**
Copyright (C) powturbo 2013-2018
GPL v2 License
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, or
(at your option) any later version.
... |
abe44873b5af2ea68ea1d281d915b2800f1832f846d2c05442a4711adbe6f269 | C | 22,715 | 640 | /* infback.c -- inflate using a call-back interface
* Copyright (C) 1995-2016 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/*
This code is largely copied from inflate.c. Normally either infback.o or
inflate.o would be linked into an application--not both. The interf... |
1e8e6fc8920264cc24da8a98637d385472351e4301e631adf10b46e20f56738d | C | 24,296 | 779 | /***********************************************************************
* mexsvec.c : C mex file
*
* x = mexsvec(blk,A,isspx,type);
*
* Input: A = nxn matrix
* isspx = 0, store x as a dense vector
* 1, store x as a sparse vector.
* type = 0, stack upper triangular part of ... |
704e273f65b62c5d2eb06d5bb10c4ccffba56544aa477f0e3957e2296c501b78 | C | 24,338 | 572 | /* enough.c -- determine the maximum size of inflate's Huffman code tables over
* all possible valid and complete Huffman codes, subject to a length limit.
* Copyright (C) 2007, 2008, 2012 Mark Adler
* Version 1.4 18 August 2012 Mark Adler
*/
/* Version history:
1.0 3 Jan 2007 First version (derived from c... |
4a1baffc6f61a5dda8855904ea00d2da9ab9f488e25c71e3c3d46e17ce6e8848 | C | 24,475 | 642 | #include "htslib/vcfutils.h"
int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which)
{
int i;
for (i=0; i<line->n_allele; i++) ac[i]=0;
// Use INFO/AC,AN field only when asked
if ( which&BCF_UN_INFO )
{
bcf_unpack(line, BCF_UN_INFO);
int an_id = bcf_hdr_id2int(header, BCF_DT_ID, "AN");
i... |
f654f3fcc74b33bd95cda63d13fe0ce589bcfe965544e0c17ee597d75efbd090 | C | 24,723 | 671 | /* infcover.c -- test zlib's inflate routines with full code coverage
* Copyright (C) 2011, 2016 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/* to use, do: ./configure --cover && make cover */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
... |
a557bf0a7d502622ac697f09da9bcf052fecb50469a32c5d98d595b5ab1d90d1 | C | 25,054 | 1,063 | /* THIS FILE IS AUTOMATICALLY GENERATED, DO NOT EDIT! */
/* Copyright (c) 2013-2014 Yoran Heling
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 lim... |
d68b088d82ca08ec3658df434b38ab162251d5f438f60db3ca0844b57c3db6eb | C | 25,089 | 569 | /* ************************************************************
% [ADA,absd] = getada3(ADA, A,Ajc1,Aord, udsqr,K)
% GETADA3 Compute ADA(i,j) = (D(d^2)*A.t(:,i))' *A.t(:,j),
% and exploit sparsity as much as possible.
% absd - length m output vector, containing
% absd(i) = abs((D(d^2)... |
f6447a7b76dd865df5e7a9919cae19b20c068fc13ceb227dd24d7414a9451edf | C | 25,197 | 558 | /*
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept. Econometrics & O.R., Tilburg University, the Netherlands.
% Supported by the Netherlands Organization for Scien... |
bb213c8054968bd97b504431168fd9c59504b8a8a6a149a42b2b2a9a2631e018 | C | 25,569 | 700 | ///////////////////////////////////////////////////////////////////////////////////////////////////
//
// Copyright (C) 2003-2005 Neuroshare Project
//
// This is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Softwar... |
27864171184b910da14ad55b27e48a1a88c96b5b41e55aceafb74077ce7a0a8b | C | 25,890 | 620 | #define _GNU_SOURCE
#include <assert.h>
#include <errno.h>
#include <math.h>
#include <string.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include "htslib/sam.h"
#include "htslib/khash_str2int.h"
#include "kvec.h"
#include "medaka_bamiter.h"
#include "medaka_common.h"
#include "m... |
d60ca6eb0a3e62ee7fb4a1ab69e8d1525ff06b06ce46889cbdfc13fb8f7534c2 | C | 25,943 | 702 | /* gun.c -- simple gunzip to give an example of the use of inflateBack()
* Copyright (C) 2003, 2005, 2008, 2010, 2012 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
Version 1.7 12 August 2012 Mark Adler */
/* Version history:
1.0 16 Feb 2003 First version for testing of... |
dadd47cc8fc7f19b76883954632ffad5839cd26d22c576669202b8fe875bc848 | C | 26,022 | 701 | #include "_cmmcost_omp.h"
double ift(double x, void * params) {
Parameters pars = *(Parameters *) params;
double neg_half_x2 = -0.5*x*x;
double res = cos(pars.omega*x)*exp(neg_half_x2*pars.s02)/M_PI; // move /M_PI out
for(size_t i=0; i<pars.n; i++) {
res *= 1 + pars.p[i]*(exp(neg_half_x2*pars.... |
92f7f1e80863354205017415d8cf57fa53e1f773ced0ab7f1378232774c9cc29 | C | 27,977 | 912 | // FilterX.c
// FilterX - Fast C-Mex filter
// [Y, Z] = FilterX(b, a, X, Z, Reverse)
// INPUT:
// b, a: Filter parameters as DOUBLE vectors. If the vectors have different
// lengths, the shorter one is padded with zeros.
// X: Signal as DOUBLE or SINGLE vector or array. The signal is filtered along
// the... |
4cc82311770e493669796a1f99701cff5df011e12ed715e156e65262f4a2e63f | C | 28,121 | 1,222 | /*
Copyright (c) 2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list o... |
b4f011a0c148f059e86afc8ad6376af0bbe8c5ebc163748ff74e8c8d03968924 | C | 29,494 | 741 | /*
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept. Econometrics & O.R., Tilburg University, the Netherlands.
% Supported by the Netherlands Organization for Scient... |
8aec9c146019a554780d298872395eb990823279566fc6e4494ba82af291a8db | C | 31,241 | 919 | // GetMD5.c
// GetMD5 - 128 bit MD5 checksum: file, string, array, byte stream
// This function calculates a 128 bit checksum for arrays or files.
// Digest = GetMD5(Data, Mode, Format)
// INPUT:
// Data: File name or array.
// Mode: CHAR to declare the type of the 1st input. Not case-sensitive.
// ... |
27871beb0e540f1e13921f781af079f94a818e20c1c9acea3ea1031b3a7e7684 | C | 31,551 | 1,085 | /* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
2011 Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to dea... |
0b239cd76daa397a00802d39925e3719f8da1cd2f1208fc66bf238881065f9f9 | C | 34,906 | 1,158 | /* ordmmd.f -- translated by f2c (version 19951025).
You must link the resulting object file with the libraries:
-lf2c -lm (in that order)
*/
#include <mex.h>
typedef mwSignedIndex integer; /* removed "long" */
/* *********************************************************************** */
/* ***... |
2b8fe9d8db2ee60710a1bfc6aa2513172dab02374bdae29d4ee37d49ebdeae07 | C | 35,131 | 1,027 | /*-----------------------------------------------------------------------------------------------*/
/* This file provides functions need to be implemented for Kilobot in order to work on the */
/* Kilogrid to test symmetry breaking two options with self-sourced noise and social interaction*/
/*------------------... |
693ff3697a838eed4646afd73c93df93c44ad627ab7cf4b15db4b28a3443ba0d | C | 35,392 | 770 | /*
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept. Econometrics & O.R., Tilburg University, the Netherlands.
% Supported by the Netherlands Organization for Scient... |
79529d33e76ace0c5367c54da36c07f2ca9fcda74d9f2c01b5f3ccad76583b41 | C | 36,825 | 847 | /*
% [Lden,L.d] = dpr1fact(x, d, Lsym, smult, maxu)
% DPR1FACT Factor d[iag] p[lus] r[ank] 1:
% [Lden,L.d] = dpr1fact(x, d, Lsym, smult, maxu)
% Computes fi and d such that
% diag(d_IN) + x*diag(smult)*x' =
%(PI_{i=1}^n L(p_OUT^i,beta_i)) * diag(d_OUT) * (PI_{i=1}^n L(p_OUT^i... |
6d0eef92e115a42e570b79d8b07a04af5ccbd6b3f3fbca9cbc61c49db9c9df43 | C | 37,883 | 840 | /*
* puff.c
* Copyright (C) 2002-2013 Mark Adler
* For conditions of distribution and use, see copyright notice in puff.h
* version 2.3, 21 Jan 2013
*
* puff.c is a simple inflate written to be an unambiguous way to specify the
* deflate format. It is not written for speed but rather simplicity. As a
* side b... |
65817d5ea8b25ab7249432d12d98316c08a76a79fdab973705b62d5bb8b888dd | C | 38,473 | 1,326 | #include <zlib.h>
#include <ctype.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <fcntl.h>
#include <errno.h>
#include <sys/stat.h>
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "version.h"
#include "htslib/kseq.h"
#define KS_BGZF 1
#... |
24b8bda691d6e39acd258c5545068e04f24be3f89ab2174a0088b758c1b348d3 | C | 38,694 | 1,183 | #include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <limits.h>
#include <errno.h>
#include <ctype.h>
#include <sys/stat.h>
#include "htslib/synced_bcf_reader.h"
#include "htslib/kseq.h"
#include "htslib/khash_str2int.h"
#define MAX_CSI_COOR 0x7fffffff // maximum indexable coordinate of .csi
typede... |
6f266f3c7e0faca653256d0189c0f00d7dc0b062d02e25df4e1202e49369595c | C | 40,608 | 1,157 | /* inffas86.c is a hand tuned assembler version of
*
* inffast.c -- fast decoding
* Copyright (C) 1995-2003 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*
* Copyright (C) 2003 Chris Anderson <christop@charm.net>
* Please use the copyright conditions above.
*
* Dec-29-2003... |
433d34b71b4e769ece1cceb8bd7d902d2c0a24ccd7550ab1856a5ba87f84f835 | C | 41,479 | 1,059 | /*
* gzlog.c
* Copyright (C) 2004, 2008, 2012, 2016 Mark Adler, all rights reserved
* For conditions of distribution and use, see copyright notice in gzlog.h
* version 2.2, 14 Aug 2012
*/
/*
gzlog provides a mechanism for frequently appending short strings to a gzip
file that is efficient both in execution ... |
30bc665af812054ca6e20a60b8c4e0b2e719103187717fd95f0b201d10e3069a | C | 41,866 | 1,208 | /*-----------------------------------------------------------------------------------------------*/
/* This file provides functions need to be implemented for Kilobot in order to
work on the */ /* Kilogrid with self-sourced noise and social interaction*/
/*---------------------------------------------------------------... |
06b5f71b248a5ae943f793922185aa2366350456d7afeda2f9f3485b0ce286d3 | C | 43,006 | 1,764 | /*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this l... |
f2a5f949ea70dde7c23a54c793aeed630a03df4bb72417cd3aa008000c44699b | C | 43,761 | 1,203 | /* trees.c -- output deflated data using Huffman coding
* Copyright (C) 1995-2017 Jean-loup Gailly
* detect_data_type() function provided freely by Cosmin Truta, 2006
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/*
* ALGORITHM
*
* The "deflation" process uses several Huffman... |
18627dd2130b1eba797427b30938e79333bdd9b74f7193767b847f200b1ec5ce | C | 50,987 | 1,428 | /*-----------------------------------------------------------------------------------------------*/
/* This file provides functions need to be implemented for Kilobot in order to work on the */
/* Kilogrid to test symmetry breaking two options with self-sourced noise and social interaction*/
/*------------------... |
8b6c599c3563c14c447c47db0d7dc9a16e8c246a078ec95a169ddcebaaebd811 | C | 54,800 | 1,561 | /* inflate.c -- zlib decompression
* Copyright (C) 1995-2016 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/*
* Change history:
*
* 1.2.beta0 24 Nov 2002
* - First version -- complete rewrite of inflate to simplify code, avoid
* creation of window when not needed, ... |
ec9101874c9a528952759b65136bce1073553e0e66dbf48eac92c32f9a86699f | C | 55,310 | 1,797 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <ctype.h>
#include <zlib.h>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "htslib/khash.h"
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
typedef khash_t(s2i) sdict_t;
/********... |
beab66fd03a97588497594c549ecb45c2176274c743f2b499047f85b05593e12 | C | 55,614 | 1,481 | /*************************************************************************************
*
* MATLAB (R) is a trademark of The Mathworks (R) Corporation
*
* Function: mtimesx
* Filename: mtimesx.c
* Programmer: James Tursa
* Version: 1.40
* Date: October 4, 2010
* Copyright: (c) 2009,... |
569a2c861c3d53e9c42db54fc91f9da2d09bc251579b94611c56d1890aa3a0e6 | C | 57,442 | 2,138 | /*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this l... |
00f403cb7810578b4b2687dd55fb132c850c3630fba2f3704a8ab896fcc8209a | C | 65,842 | 2,007 | /* zip.c -- IO on .zip files using zlib
Version 1.1, February 14h, 2010
part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modifications for Zip64 support
Copy... |
497adf676b1cae2a7afa834e4aba86383f7b697f5fdd03a8179ea9024a431cf9 | C | 71,055 | 2,125 | /* unzip.c -- IO for uncompress .zip files using zlib
Version 1.1, February 14h, 2010
part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modifications of Unzip for Zip6... |
ce1831c1fd09a06c3a82f107fc292309bca49f5a9c3a870db8f6ea06eae9fd28 | C | 71,292 | 2,468 | /* Based on src/http/ngx_http_parse.c from NGINX copyright Igor Sysoev
*
* Additional changes are licensed under the same terms as NGINX and
* copyright Joyent, Inc. and other Node contributors. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this softwar... |
41d9758226a547ba4d6296e32e05345c8b09512874d4afbb889494ba610d9bb1 | C | 72,369 | 2,630 | /*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this l... |
e0f9f6edace805d1590ac9a184d8c6e9a86b1d43e5dccdb5f4f7303617e82ac1 | C | 76,408 | 2,357 | /*
* MATLAB Compiler: 2.0.1
* Date: Fri Feb 4 11:20:20 2000
* Arguments: "-mw" "mtcsd"
*/
#include "dpss.h"
#include "dpssdir.h"
#include "dpssload.h"
#include "fftfilt.h"
#include "sinc.h"
#include "signal_private_tridieig.h"
#include "signal_private_tridisolve.h"
static double __Array0_r[1] = { 0.0 };
static ... |
304aacc524008f7523826aeb5204b0028ff58b5452cd3a926810976ab795f211 | C | 76,757 | 3,207 | /*
* Copyright 1996-2006 Catherine Loader.
*/
#include "mex.h"
/*
* Copyright 1996-2006 Catherine Loader.
*/
#include <math.h>
#include "mut.h"
/* stirlerr(n) = log(n!) - log( sqrt(2*pi*n)*(n/e)^n ) */
#define S0 0.083333333333333333333 /* 1/12 */
#define S1 0.00277777777777777777778 /* 1/360 */
#defin... |
7f0dcceb996e09d9359528deab3c628736cc7ff23556a82a160056dc3d003a75 | C | 76,761 | 3,207 | /*
* Copyright 1996-2006 Catherine Loader.
*/
#include "mex.h"
/*
* Copyright 1996-2006 Catherine Loader.
*/
#include <math.h>
#include "mut.h"
/* stirlerr(n) = log(n!) - log( sqrt(2*pi*n)*(n/e)^n ) */
#define S0 0.083333333333333333333 /* 1/12 */
#define S1 0.00277777777777777777778 /* 1/360 */
#defin... |
e86860279d2cbabb0e5823808d35027f83fc9ed83fc4cd2a04d9ae735668e2dc | C | 76,786 | 3,208 | /*
* Copyright 1996-2006 Catherine Loader.
*/
#include "mex.h"
/*
* Copyright 1996-2006 Catherine Loader.
*/
#include <math.h>
#include "mut.h"
/* stirlerr(n) = log(n!) - log( sqrt(2*pi*n)*(n/e)^n ) */
#define S0 0.083333333333333333333 /* 1/12 */
#define S1 0.00277777777777777777778 /* 1/360 */
#defin... |
a154edbb09dba561fd28f2beb0b0f415d11e784c6392c5aa933517900379611c | C | 77,438 | 2,297 | /* symfct.f -- translated by f2c (version 19951025).
You must link the resulting object file with the libraries:
-lf2c -lm (in that order)
*/
#include "mex.h"
typedef mwSignedIndex integer; /* removed "long" */
#if !defined(max)
#define max(A, B) ((A) > (B) ? (A) : (B))
#endif
/* **********... |
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