sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c10639b5890e3603e2033f3f53e67f85ddd6e82f2f3b802a8aedecbb652f5776 | C | 7,002 | 256 | /* test/pileup.c -- simple pileup tester
Copyright (C) 2014,2018-2019 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software with... |
59c9d0dc5d30e87ac01269f4746c68065195cbe5adf95aebe40922e48ce63842 | C | 7,004 | 278 | /*
** Read input data into array
**
** G.Lohmann, MPI-KYB, 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_bl... |
680420a6f93aa84d78e82bf64677e65d3f311b3de153014ac05f569485d7da44 | C | 7,009 | 194 | /* sam_opts.c -- utilities to aid parsing common command line options.
Copyright (C) 2015, 2019 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to... |
90627bad758df610a04b89429fb11344592d15d564686c908f62cf7259ad398d | C | 7,030 | 284 | /****************************************************************
*
* vpreprocess: FreqFilter.c
*
* Copyright (C) Max Planck Institute
* for Human Cognitive and Brain Sciences, Leipzig
*
* <[email protected]>
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the... |
864ffafdbea335844b5a7b9d4f9fbc0bdece0a89fd628439b507d28d53a2f4e3 | C | 7,036 | 226 | /*
Copyright (c) 2012-2014, 2016, 2018, 2020 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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... |
4b88749682bbfd9f5a51f75c0f47d0d47c61fda517dcc87f9b4fda317461ec4f | C | 7,064 | 204 | /*
Copyright (C) 2018-2019 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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 withou... |
b931eb5a7cb67c5cc55fef8c1bc95a8fa34226c9f5a4b4c7a00409b3cbe2cf99 | C | 7,081 | 225 | /* test/pileup_mod.c -- simple pileup tester with base modifications
Copyright (C) 2020 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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... |
8d4e425952a3a39cacf37c8fb83c6b84aa9e89d63aa248dfc3463155d4836a3f | C | 7,315 | 290 | /* Tests for CRAM-3.0 rANS codec */
/*
* Copyright (c) 2019,2020 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must reta... |
574299243b07b613f4863ce7d98dda08cbf30d6d7ffebdb13a5965caceb782b9 | C | 7,336 | 228 | /* maq2sam.c -- convert MAQ output to SAM.
Copyright (C) 2008, 2009, 2018 Genome Research Ltd.
Author: Heng Li <[email protected]>
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... |
d853a2348a0d30163aec942a868a2ae7e5f1940f572fd1e888b3a2622f25f4b7 | C | 7,402 | 296 | /* Arithmetic coder tests */
/*
* Copyright (c) 2019,2020 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
5d2dec4851a4391862bd9135fd01dca74f9799f2d532de32d89212f22887c4e4 | C | 7,438 | 360 | /*! \file
Topological classification.
Each foreground voxel of a 3D binary input image receives a
label indicating its topological type. Possible types are
the following:
Output codes:
<ul>
<li> 1: interior point
<li> 2: isolated point
<li> 3: border point
<li> 4: curve point
<li> 5: curves junction
<li> ... |
6f2f16cd304e3eb2227d9b10166bed80fb0d4a2429ab2a12e8ea080268a0adb2 | C | 7,510 | 230 | /* bam_rmdupse.c -- duplicate read detection for unpaired reads.
Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
Portions copyright (C) 2009 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and ass... |
1698214844c404fd87beac3c1a56db74c77603e93e1589520218c45df7904687 | C | 7,556 | 246 | /* bam_index.c -- index and idxstats subcommands.
Copyright (C) 2008-2011, 2013-2016, 2018, 2019 Genome Research Ltd.
Portions copyright (C) 2010 Broad Institute.
Portions copyright (C) 2013 Peter Cock, The James Hutton Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, fre... |
b876378b4993839823c9ef5b4b56ba12e29480a1d7a50f467401ae3ad250e3e0 | C | 7,668 | 295 | /*
** compute correlation matrix
**
** G.Lohmann, Feb 2011
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_sort.h>
#include <gs... |
134f07ef0e3afb677e08ffd5cdb30c830b35bd8e25bd7d5af2eb904e2690f6f9 | C | 7,744 | 276 | /* region.c -- Functions to create and free region lists
Copyright (C) 2019 Genome Research Ltd.
Author: Valeriu Ohan <[email protected]>
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 ... |
8133c0737614c54214308e42a63bc70123e48614a679849a16585fccee91471b | C | 7,766 | 333 | /**
* @file test.c
* @brief test program for 32-bit and 64-bit output of SFMT.
*
* @author Mutsuo Saito (Hiroshima-univ)
*
* Copyright (C) 2012 Mutsuo Saito, Makoto Matsumoto, Hiroshima
* University and The University of Tokyo.
* All rights reserved.
*
* The new BSD License is applied to this software, see L... |
29d7b3cb1857f41bde9b0779b0e70120a57b07d01add56954061dfc5c2c65fdf | C | 7,770 | 311 | /* Tests for 4x16 rANS codec */
/*
* Copyright (c) 2019,2020 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain t... |
4f259f0fcfb43d89a751b9c7bd285536e0cc6b47ad6066992ae86217180445a6 | C | 7,792 | 231 | #include <mex.h>
#include <stdlib.h>
#include <string.h>
#include "compiler.h"
#if defined (COMPILER_MSVC)
#include <math.h>
#define isnan _isnan
#define INFINITY (HUGE_VAL+HUGE_VAL)
#define NAN (INFINITY - INFINITY)
#elif defined(COMPILER_LCC)
#include <math.h>
#define INFINITY (DBL_MAX+DBL_MAX)
#define NAN (INFINITY... |
76434a767cfbfc2ca07343371cb7f200c829ddf7f49726d10c71a3150283fa96 | C | 7,892 | 312 | /** \file znzlib.c
\brief Low level i/o interface to compressed and noncompressed files.
Written by Mark Jenkinson, FMRIB
This library provides an interface to both compressed (gzip/zlib) and
uncompressed (normal) file IO. The functions are written to have the
same interface as the standard file IO functi... |
1efb47740e55e342a0e82f7b4b81517047d8bc77bf463b8a91eb669fcb0099f1 | C | 7,944 | 352 | /*
* $Id: ReadPnm.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains routines for reading portable anymap (PNM) files.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is h... |
c827817258ef56a77adb1bc82e11b4078687684b759d3f5fe9420ee559a064c4 | C | 7,951 | 298 | /*
** ECM - eigenvector centrality mapping
**
** G.Lohmann, MPI-KYB, updated Oct 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_math... |
e0875d1ead952ad1729580136d05d95d67506a08d130fef9140d02e1dea45d6c | C | 7,969 | 380 | /*! \file
check if simple point.
check if the given voxel is a simple point.
A point is simple, if its deletion does not alter
the topology.
This function is used in topological thinning (VThin3d).
It returns 1, if simple point; it returns 0, otherwise.
\par Reference:
G. Bertrand, G. Malandain (1994):
"A new chara... |
6c673ff869b56479c1ba2bc360926fee68d67201d86257402c702a5c0c384032 | C | 8,007 | 271 | /* htsfile.c -- file identifier and minimal viewer.
Copyright (C) 2014-2018 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Softwar... |
16a6d718d1da90199d0cb28060c9c7108ee880ae03a59bbf0131559d3abd43b9 | C | 8,051 | 379 | /*
* $Id: List.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains the routines for manipulating VList instances.
*
* [Thanks to Murray Goldberg ([email protected])]
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this softw... |
707097d13958c56ff77e2fedfa11dd8a5bc3ef96fab2029a7f0da0758732a6d4 | C | 8,075 | 239 | /* stats_isize.c -- generalised insert size calculation for samtools stats.
Copyright (C) 2014, 2018 Genome Research Ltd.
Author: Nicholas Clarke <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software... |
fa23d0201f9bb7aa069cef908631ab869dc172eb7926fb6fd533e12f6504c69d | C | 8,098 | 342 | /*! \file
3D connected component labelling
Each foreground voxel receives a label indicating
its membership in a connected component.
The algorithm is based on depth first search.
\par Reference:
G. Lohmann (1998). "Volumetric Image Analysis",
John Wiley & Sons, Chichester, England.
\par Author:
Gabriele Lohmann, ... |
5f1e702178f23af140f742bcb54df487abc44ce015feea8dbd7d534c8886533f | C | 8,156 | 373 | /*! \file
Compute 3D shape features and moments.
The following functions compute several shape features, including
central moments, center of gravity, and volume size.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
/* From the Vista library: */
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <via/via.h>
#inclu... |
e0181b5b57fb8b397a9c4eac982afec3b23d841c71f8506e71723423b32fe361 | C | 8,247 | 303 | /*
* dot dot product
* cross cross product
* determinant determinant of matrix built from three vectors
* pdist distance from point towards origin
* ppdist distance between two points
* plinproj projection of point onto line spanned by two points
* ptriproj projection of point onto plane spanned by three point... |
ac5398d6c5ba5660f80ddab591ca6b101bbdbcd11ea0e61c4e78fdbdb1cc775a | C | 8,266 | 348 | /*
** cylarim: cylinder-based laminar fMRI analysis
**
** G.Lohmann, MPI-KYB, Nov 2024
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gs... |
c629b3a9116b75f79bf04174c0d9b826ffe73bb885bf44c83139a1cb9e7defe4 | C | 8,308 | 231 | /**************************************************************************
* Microsoft COCO Toolbox. version 2.0
* Data, paper, and tutorials available at: http://mscoco.org/
* Code written by Piotr Dollar and Tsung-Yi Lin, 2015.
* Licensed under the Simplified BSD License [see coco/license.txt]
****************... |
434d7fe9f4ae6ba560c83034ebd0e65d75121146453535153dd5c3830ac90c87 | C | 8,387 | 299 | /*
** compute edge densities
**
** G.Lohmann, Feb 2015
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_sort.h>
#include <gsl/gs... |
b37fd619b6a36c3a008bee4ca2be48a58d9c68fc2ff45f257f848d5b893b155f | C | 8,406 | 266 | /* multipart.c -- GA4GH redirection and multipart backend for file streams.
Copyright (C) 2016 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to ... |
5395bc091b6439d0f37f92ce60f86a595ae3e52e09070dd5d013d4930858c9dd | C | 8,419 | 388 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
#include <stdio... |
4ca1fb67dfcea4829d51345509ab054786907f0d51b43d34a4524dc9b6919780 | C | 8,457 | 380 | /*! \file
3D Deriche filter for edge detection
\par Reference:
R. Deriche. Fast algorithms for low-level vision.
IEEE Transactions on Pattern Analysis and Machine Intelligence,
1(12):78-88, January 1990.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
/* From the Vista library: */
#include <viaio/Vlib.h>
#include <via... |
93e81ddf69dad4691e65d26342edcd84d107789398419267d1937e78c171b095 | C | 8,488 | 288 | /****************************************************************
*
* Copyright (C) Max Planck Institute
* for Biological Cybernetics, Tuebingen, Germany
*
* Author: Gabriele Lohmann, 2015
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public Lic... |
d1c4582894513749ec958a7ac0a640a2250e4c0b9d178b054c55e11b5f4d6087 | C | 8,488 | 267 | /* multipart.c -- GA4GH redirection and multipart backend for file streams.
Copyright (C) 2016-2017 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software")... |
84a87b2482b1bd3d84c9fae0a599e810907a0356bf5a890df831d7c368f54ade | C | 8,615 | 257 | #include <mex.h>
#include <stdlib.h>
#include <string.h>
#include "compiler.h"
#if defined (COMPILER_MSVC)
#include <math.h>
#define isnan _isnan
#define INFINITY (HUGE_VAL+HUGE_VAL)
#define NAN (INFINITY - INFINITY)
#elif defined(COMPILER_LCC)
#include <math.h>
#define INFINITY (DBL_MAX+DBL_MAX)
#define NAN (INFINITY... |
d04027905624984ed0dd862d6c6aa4eeec9c0bb82a8ce66926776d343d54ef37 | C | 8,829 | 349 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* File Name : stm32f4xx_hal_msp.c
* Description : This file provides code for the MSP Initialization
* and de-Initialization codes.
****************************... |
49e75613f86af20f5e6469f8574d6a30e6d074257e16e7fca790622eb1cc92f1 | C | 8,852 | 297 | /*
** Cylam: Cylinder-based Algorithm for Laminar fMRI Data Analysis
**
** G.Lohmann, MPI-KYB, Oct 2024
*/
/* From the standard C library: */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
/* From the Vista library: */
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/m... |
16dd8ade50caf8bb2d5678db345ad70941a2726d121d4fd65beee6f1ab837dd7 | C | 8,866 | 462 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
#include <limit... |
7db3866b57bf2d6ddd27cd758882fd5c4324a88eb9139956385f81880193b252 | C | 8,892 | 225 | /* test/test_str2int.c -- Test integer string conversion (and safe printing)
Copyright (C) 2019-2020 Genome Research Ltd.
Author: Rob Davies <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to d... |
18410ef358417138759c6d60c60adb09bdb2f32c6cb48f9693133096376c785d | C | 8,899 | 257 | /* cut_target.c -- targetcut subcommand.
Copyright (C) 2011 Broad Institute.
Copyright (C) 2012-2013, 2015, 2016, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files ... |
ba1d60374b847ed3f42ff6a6ab11b63f8fcd15ec648dfe8a5b8ded5a063721f7 | C | 8,964 | 203 | /* test/test-bcf-translate.c
Copyright (C) 2017-2018 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
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 res... |
e955f0ad843cb28156881145087164fd37f1d6f4682ae4b62f224e465642e469 | C | 8,984 | 409 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
#include "vote.... |
d8f11c02ce1c627c6943b4b2e5edc7e6c0c7ddb6f9a7e8f6cd421a7245a2a249 | C | 9,084 | 306 | /*
* Copyright (C) 1999-2022 Christophe Phillips
*/
/*
Input : ind_tr, XYZv, weight, defl, tri_pt4
Output : Cii_lin
weight = (sig1-sig2)/((sig1+sig2)*2*pi) ;
*/
#include <math.h>
#include "mex.h"
#define NR_NEIGH_TRI 10 /* Max # of triangle neighbours */
void Cii_constant(double C[], double ind_tr[], int N... |
e2138d63780e6412b1012b3e4edd01a4d3bf707ddddb9df402f575af06c38235 | C | 9,091 | 398 | /*
* Copyright (c) 2019 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* t... |
5648265385be3641834f07a54ee6c9bb77575531495290d19703107f0814d016 | C | 9,166 | 282 | /* The MIT License
Copyright (C) 2010, 2013 Genome Research Ltd.
Copyright (C) 2011 Attractive Chaos <[email protected]>
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 ... |
04cce67dc83a9e829cb2a306b724d45b853f55898e354b40ee46df57d689a5ac | C | 9,171 | 378 | /*
** read/write nifti-1 to vista format
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <strings.h>
#include <math.h>
#include <nifti/nifti1.h>
#include <nifti/nifti1_io.h>
#define MIN_HEADER_SIZ... |
f4ae10c17406a27870a28dbf31c3efed53d54e1e089612994be48cc8eb66bc82 | C | 9,177 | 302 | /*
** Implementation of LISA algorithm
** for statistical inference of fMRI images
**
** 2nd level inference (one-sample test)
**
** G.Lohmann, 2017
*/
#include <viaio/Vlib.h>
#include <viaio/file.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <viaio/os.h>
#include <viaio/VImage.h>
#include <gsl/gsl_cdf.h... |
366916a9102d73b5688fae6e526c7379fd9325da933376557552bb635be8bee7 | C | 9,224 | 349 | /*
** CCM - connectivity consistency mapping
**
** G.Lohmann, July 2010
*/
#include <viaio/Vlib.h>
#include <viaio/file.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <viaio/os.h>
#include <viaio/VImage.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <stdio.... |
e90f994a1702f14abfea00f30778474a40457df62ca7573a5573e13b059f156e | C | 9,291 | 422 | /*
* $Id: ConvertR.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains a routines for converting an image from one pixel
* representation to another by mapping the full range of source pixel
* values to the full range of destination pixel values.
*/
/*
* Copyright 1993, 1994 University of British... |
b7a7a7624763fc8572738a4055db2e1c3a3c592d3cc64df83d10fb8cb255a923 | C | 9,317 | 395 | /* The MIT License
Copyright (C) 2011 by Attractive Chaos <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation t... |
0f1f4aa59af21620facb36b688dd9fd5b19e345cc4b9f8b99102092892f7c9ff | C | 9,402 | 389 | /*
** hemodynamic modelling for single-subject LISA
**
** G.Lohmann, MPI-KYB, 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <gsl/gsl_cblas.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.... |
233f476a570b3ef98e0d5e1e09219127fb9647fc4511255d88701e53788c96dc | C | 9,413 | 395 | /* textutils.c -- non-bioinformatics utility routines for text etc.
Copyright (C) 2016 Genome Research Ltd.
Author: John Marshall <[email protected]>
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 ... |
6b2b70d7270c71a719cbbeab094d77069568f726125a3de17a207eab626be3ad | C | 9,607 | 329 | /* htsfile.c -- file identifier and minimal viewer.
Copyright (C) 2014-2019 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Softwar... |
0cfbe0c31657130e40ca8462522fce1d655a2b58a986a440b69e700a9ff6cb28 | C | 9,617 | 386 | /*
* John Ashburner
* Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
*/
#define _LARGEFILE_SOURCE
#define _LARGEFILE64_SOURCE
#define _FILE_OFFSET_BITS 64
#include <math.h>
#include <fcntl.h>
#include <sys/stat.h>
#include <stdlib.h>
#include <stdio.h>
#include "mex.h"
#ifdef SPM_WIN32
#include <wi... |
8f5cc0b5dfb68ba2477428dc6b5f42ef5326d398d92122c0db352cf4dbfdcf10 | C | 9,876 | 370 | /*! \file
3d chamfer distance transform.
For each background voxel, the length of the shortest
3D path to the nearest foreground voxel is computed.
The chamfer distance metric is an approximation to the
Euclidian distance.
\par References:
G. Borgefors (1984).
"Distance Transforms in arbitrary dimensions",
CVGIP 27, ... |
fa74538cfcdb2fb45fbbd5fd3347d3147ec9bfb59ab8d220ad91de5ec528b920 | C | 9,877 | 483 | /*! \file
3D Skeletonization
Perform a topological thinning.
\par Reference:
A.Manzanera,T.Bernard,F.Preteux,B.Longuet:
"nD skeletonization: a unified mathematical framework".
Journal of Electronic Engineering, Vol. 11-1, Jan. 2002, pp.25-37.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
#include <stdio.h>
#inclu... |
548d932cdda09ca2abe7a74fd9425efa8c8401c1279e2b1779a861ecd455a99e | C | 9,926 | 272 | /* bedcov.c -- bedcov subcommand.
Copyright (C) 2012 Broad Institute.
Copyright (C) 2013-2014, 2018-2021 Genome Research Ltd.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software... |
d96b91a90393c79c801e9d9c5489638decd442954126c234e2b4b9710d9ec78d | C | 10,049 | 450 |
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <gsl/gsl_cblas.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_sort.h>
#... |
9481fe4dc91902dac56bcb9b24d4e2a391769899a2440ca3629632a2e310279d | C | 10,153 | 301 | /*
* $Id: Shear.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains routines for shearing images.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby granted without ... |
ef7fd84b7ad1a4e57e141f06878a276053385ac549c5a7f1c4e00028bc7a1637 | C | 10,190 | 342 | /*
Copyright (C) 2014 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
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 limit... |
a8ce9d0585580738a05b83582ada5c0d57bb8364c39e7fc46a08c5e5a42fdd30 | C | 10,195 | 450 | /*
** Various methods for normalizaing data
**
** G.Lohmann, MPI-KYB, Jan 2020
*/
#include "viaio/Vlib.h"
#include "viaio/VImage.h"
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_sort.h>
#... |
6c825a6052dee153b36cbfa49b7cb3bd737cc44d9ceeff2507e5b91333dbdaa0 | C | 10,199 | 272 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu, Bioinformatics Program at Boston University.
******************************************************************************/
#include "basic.h"
/... |
abae4fdef80d63340ad10e1e420d1508f370ce6fc4c61b5bddb743be93006dd0 | C | 10,245 | 286 | /* Variable-length encoding tests */
/*
* Copyright (c) 2020 Genome Research Ltd.
* Author(s): Rob Davies
*
* 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 a... |
90cafb5a5b17a46b478770ef4abdc9a641cb395419abbb80f288138a63d44582 | C | 10,274 | 313 | /**
******************************************************************************
* @file stm32f4xx_hal_dma_ex.c
* @author MCD Application Team
* @brief DMA Extension HAL module driver
* This file provides firmware functions to manage the following
* functionalities of the DMA Extens... |
8b1dd98838fa4882028ef98fce2d465221833b559995fcffb2f0a341ea98d768 | C | 10,381 | 313 | /*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby granted without fee, provided that
* the above copyright notice appears in all copies and that both that
* copyright notice and th... |
d757a684c102dec0430034addc98056ad8e2ebace05cd7ba5a16498008ad404d | C | 10,467 | 351 | /*
* $Id: PackData.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains routines for packing and unpacking arrays of
* data elements, converting them between external and internal forms.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, a... |
946bb62e5376c4e6803490120718150a1567f80ef863c4366481b4fb0cb0ddbe | C | 10,570 | 444 | /* The MIT License
Copyright (C) 2011 by Attractive Chaos <[email protected]>
Copyright (C) 2013-2018, 2020-2021 Genome Research Ltd.
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... |
b34b5005f075d3a8e40641bbfbe04c8a5e65ee525a30599fa064f878149fd621 | C | 10,579 | 387 | /*
* Trivial amendments by James Bonfield <[email protected]> to provide an
* HTSlib interface. 2015.
*
* Externally our API uses an opaque hts_md5_context structure.
*
* Internally either this gets defined and used with the routines here
* or it remains incomplete and is cast to the OpenSSL MD5_CTX structure
* ... |
243463d32b547f318df3db1b6afca89c774d3bfd57c766ebebc5cd9bf6117e12 | C | 10,656 | 388 | /*
* Trivial amendments by James Bonfield <[email protected]> to provide an
* HTSlib interface. 2015.
*
* Externally our API uses an opaque hts_md5_context structure.
*
* Internally either this gets defined and used with the routines here
* or it remains incomplete and is cast to the OpenSSL MD5_CTX structure
* ... |
0bd16728abcde7d0dce48268264993330bc26c978b6b936a98bc2ef821810a18 | C | 10,668 | 325 | /* bam_rmdup.c -- duplicate read detection.
Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
Portions copyright (C) 2009 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation... |
99cafb04d7105d490b230ae33c638a429baa7450bfd360dd80cb4206a84a7d49 | C | 10,847 | 416 | /*
* $Id: Param.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains routines for parsing and reporting parameter values.
*/
/*
* Copyright 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby... |
fea83a02686fa6daa327373780530fa5e3932bf3bae792e030b9d8bbe93584f8 | C | 10,879 | 313 | /* The MIT License
Copyright (C) 2010, 2013-2014, 2020 Genome Research Ltd.
Copyright (C) 2011 Attractive Chaos <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Softwa... |
065865f26d3aae6c43d56bae23dcac826af2a2281d95752443b53df12b09b377 | C | 11,040 | 378 | /* bam_tview_html.c -- HTML tview output.
Copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Copyright (C) 2019 Genome Research Ltd.
Author: Pierre Lindenbaum <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of... |
3201b2cec6247d21c48c3a3184721c951a9c9c306649dd344b6df94615f47ac8 | C | 11,228 | 328 | /* bam_tview_curses.c -- curses tview implementation.
Copyright (C) 2008-2015, 2019 Genome Research Ltd.
Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person o... |
8d6316805f04b801b1151892bc3aa37e0ae48ac7dbedf0f2cbe6c4ee36c06492 | C | 11,238 | 398 | /*! \file
Geometric transformations using cubic spline interpolation.
This file contains functions for cubic spline resampling
and 3D scaling. The transformation equation is:
y = A(x-x0) + b
where x,x0,b,y are 1x3 vectors and A is a 3x3 matrix.
The vector x0 can be used to specify a position that
remains uncha... |
bd3c4621c64f64bf61c01cf97f7efc20227296590ec7dbf8c9ecbc91a674f584 | C | 11,539 | 285 | /* realn.c -- BAQ calculation and realignment.
Copyright (C) 2009-2011, 2014-2015 Genome Research Ltd.
Portions copyright (C) 2009-2011 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documen... |
dbc9640e59a578c42d4f375978a6449385f36892066c8d80fb3006588eab02c0 | C | 11,744 | 366 | /* tbx.c -- tabix API functions.
Copyright (C) 2009, 2010, 2012-2015, 2017 Genome Research Ltd.
Copyright (C) 2010-2012 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (th... |
89777686877ae692042eb1800c9bfafaf890633ac4ecf2cf917c9923b4bb2eab | C | 11,747 | 579 | /*
** gsl routines for float data type
**
** G.Lohmann, July 2004
*/
#include <viaio/Vlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <gsl/gsl_cblas.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_sort_vector.... |
a6c49e7e9d1ad21eadedb7daad2f34574e20b8bd823fc0e72357beadf9751ae5 | C | 11,783 | 493 | /*
* $Id: ConvertL.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains a routines for converting an image from one pixel
* representation to another by an abitrary lineary mapping
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sel... |
39fad1efbdff87f25461331db92f7bfc7191a5d6ab0d6a42fd6eee18328b6b76 | C | 11,819 | 255 | /* The MIT License
Copyright (c) 2011 Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use,... |
6c2123c3732d2627be853289b272f51a327c89fcb948ef0a15fae7be2b7f08df | C | 11,957 | 497 | /* textutils.c -- non-bioinformatics utility routines for text etc.
Copyright (C) 2016, 2018-2020 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), ... |
74b941fd1f7a343a48d5b139e4bd004d271b128943b55fbf088e2f6f4a3ab6e3 | C | 11,973 | 337 | /*
** Implementation of LISA algorithm
** for statistical inference of fMRI images
**
** 2nd level inference using a GLM design matrix,
** e.g. for anova designs
**
** G.Lohmann, 2018
*/
#include <viaio/Vlib.h>
#include <viaio/file.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <viaio/os.h>
#include <vi... |
fe718c5092249c7f7a79129e4a38b537350a1620eefba8640e91bf0a57bc5dc1 | C | 12,012 | 311 | /* test/hfile.c -- Test cases for low-level input/output streams.
Copyright (C) 2013-2014, 2016, 2018 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software... |
2e500d3608691eebaccc156d26030db52c4cd1b9998cb8200b1295997c0cb304 | C | 12,102 | 423 | /* test_kstring.c -- kstring unit tests
Copyright (C) 2018, 2020 Genome Research Ltd.
Author: Rob Davies <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restr... |
66df660ab5c653f278e6a06c42e332f716971ec6af4f3825199fcee51fab8fb6 | C | 12,123 | 310 | /* The MIT License
Copyright (C) 2003-2006, 2008-2010 by Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitati... |
98ceb51ef121f7e460d12615487183cfaab9d903d643c59fc6ab21153cc7e9b3 | C | 12,136 | 469 | /* Tests for fqz codec */
/*
* Copyright (c) 2019,2020 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abo... |
107d89ad348f6dcbb05852644be0199fd8d5442be50df99f4c1324599530cc4b | C | 12,143 | 526 | /*! \file
Contrast enhancement.
A piecewise-linear contrast enhancement is performed.
The contrast stretching function is derived from the mean
value and the standard deviation of the input image.
The output pixel repn need not be identical to the input
image. Thus, it is possible to convert to ubyte repn
for eas... |
4241d93041489ae59bb27b2b37131ea24df3f44a96860afa90998a7a133a3d6b | C | 12,291 | 293 | /* bamtk.c -- main samtools command front-end.
Copyright (C) 2008-2021 Genome Research Ltd.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without re... |
a49353b9e2fa98a7f855649010780885ff0939552a9c878ac68300ffdd45bccb | C | 12,397 | 408 | /*
* Copyright (C) 1999-2022 Christophe Phillips
*/
/*
Input : ind_tr, XYZv, weight, defl, tri_pt4
Output : Cii_lin
weight = (sig1-sig2)/((sig1+sig2)*2*pi) ;
*/
#include <math.h>
#include "mex.h"
#define NR_NEIGH_TRI 10 /* Max # of triangle neighbours */
void Cii_linear(double C[], double ind_tr[], int Ntr... |
eb56913d8f07635c980e2cc59d3ec90ff0ebbd43975027b54d723a4e5e1b95a6 | C | 12,473 | 311 | /* realn.c -- BAQ calculation and realignment.
Copyright (C) 2009-2011, 2014-2016, 2018, 2021 Genome Research Ltd.
Portions copyright (C) 2009-2011 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associ... |
90c8929a36fca601b612ad64fdc5e5b19e1902dc9fb6f084b246766b09bed082 | C | 12,683 | 346 | // VChooseKO.c
// VChooseKO - Permutations of K elements, (order, no repetitions) [MEX]
// VChooseKO(V, K) creates a matrix, which rows are all permutations of
// choosing K elements of the vector V with order and without repetitions.
//
// INPUT:
// V: Array of class DOUBLE, SINGLE, (U)INT8/16/32/64, LOGICAL, CHAR.
... |
f14fcb1427bc60c095cb77eae0999f9d54b178bc8e721aca9b6ca40785420c02 | C | 12,738 | 345 | #include <mex.h>
#include <stdlib.h>
#include <string.h>
#include "compiler.h"
#if defined (COMPILER_MSVC)
#include <math.h>
#define isnan _isnan
#define INFINITY (HUGE_VAL+HUGE_VAL)
#define NAN (INFINITY - INFINITY)
#elif defined(COMPILER_LCC)
#include <math.h>
#define INFINITY (DBL_MAX+DBL_MAX)
#define NAN (INFINITY... |
32cfcf384806e3d543b0071d901015e0eb8c4e65bd43b3dcd518ba303ab34bc2 | C | 12,762 | 345 | #include <mex.h>
#include <stdlib.h>
#include <string.h>
#include "compiler.h"
#if defined (COMPILER_MSVC)
#include <math.h>
#define isnan _isnan
#define INFINITY (HUGE_VAL+HUGE_VAL)
#define NAN (INFINITY - INFINITY)
#elif defined(COMPILER_LCC)
#include <math.h>
#define INFINITY (DBL_MAX+DBL_MAX)
#define NAN (INFINITY... |
ca24921f8f43b0f85c7bb99592ce5c0d691ee44060dab7fafab93184d0e7df56 | C | 12,849 | 439 | /*
** Implementation of LISA algorithm
** for statistical inference of fMRI images
**
** 2nd level inference, two-sample ttest, paired t-test
**
** G.Lohmann, MPI-KYB, 2018
*/
#include <viaio/Vlib.h>
#include <viaio/file.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <viaio/os.h>
#include <viaio/VImage.h>
... |
55429444017dfe292511bb5381e2207252027b22e0537a54e2da01e5b186534e | C | 12,999 | 437 | /**
* @file SFMT.c
* @brief SIMD oriented Fast Mersenne Twister(SFMT)
*
* @author Mutsuo Saito (Hiroshima University)
* @author Makoto Matsumoto (Hiroshima University)
*
* Copyright (C) 2006, 2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima
* University.
* Copyright (C) 2012 Mutsuo Saito, Makoto Matsumoto, H... |
ec90286b6c8e366a141bc97fcda2f842edad7d8eb94210a00c26758879474ee8 | C | 13,197 | 466 | /* hfile_s3.c -- Amazon S3 backend for low-level file streams.
Copyright (C) 2015-2017 Genome Research Ltd.
Author: John Marshall <[email protected]>
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 ... |
9ccf3cfc73a0091866f3695851bc2f34b87fbd14973880e7e3c148cebcd0de62 | C | 13,347 | 392 | /*
Copyright (c) 2015 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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 of ... |
9d1d460d1216e417093e4658164ebafe48ff44e5f2e6698770b436b7cbf3b361 | C | 13,414 | 423 | /*
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,
th... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.