sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5d4f417a6017aabdf7be6afcf6cd46ce711413cfe2df82fbb1a069fd61ce1ff3 | C | 10,595 | 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... |
456c9eeca1c23975d5542854ff4504e32d4ed00f28e5bc5cb65e1ce20e6e8043 | C | 10,635 | 394 | /*
* Copyright (c) 2019-2020, 2022 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,... |
27d9d3402062a1f43e81eb47be2f0351b65ed6db34c113c33c10120da97893e2 | C | 10,646 | 347 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
384e4405b79988f20bffae2dd76f72275c83aa10766f5a554cbca2e523707402 | C | 10,653 | 308 | /* dgtsv.f -- translated by f2c (version 20061008). */
#include <math.h>
#include <stdio.h>
//inline double ABS(double a) { return fabs(a); }
//inline double MAX(double a, double b) { return fmax(a,b); }
#define ABS(a) fabs(a)
#define MAX(a,b) fmax(a, b)
int dgtsv_patch(int *n, int *nrhs, double *dl, double *d__, d... |
fd89006baa6308ec70bb77c89cad7cf917004ee4aabe43e66660645636451bb1 | C | 10,664 | 358 | # /*##########################################################################
#
# Copyright (c) 2019 European Synchrotron Radiation Facility
#
# 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... |
5ffbc0db18cc1323ee602445cc5ea3fda0e62fbc53795f76fbd11da48d8d352f | C | 10,671 | 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
* ... |
9e1ec901b37cc88477686c51d2ebaf6a20cf6de713168f133615c8b191d07776 | C | 10,692 | 354 | /******************************************************************************
* malloc_count.c
*
* malloc() allocation counter based on http://ozlabs.org/~jk/code/ and other
* code preparing LD_PRELOAD shared objects.
*
******************************************************************************
* Copyright ... |
c2f83cc0f6438869d57d0eb6be9644c9e6b000119d20f2c4ceda857e1a275ad0 | C | 10,708 | 309 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
d7203429973258a7a138ab88567abfe1909266249f00b28d599e2ae3424a738a | C | 10,712 | 411 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 Li... |
00863d8640b158307b07caede3353849a0749294e72be3dbe9b7aba6785d13cf | C | 10,774 | 395 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
4083ff2b0cf6094edbef5db7761441d257eff820781e3212bc94daaad0bbf556 | C | 10,780 | 242 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
cd78597d82344cad28b9f8da12849584e8f6a1e71bd9ebbe1c76c9276495e21f | C | 10,783 | 231 | /*
* Simple Matlab mex wrapper for NIFTI-1 reference code.
*
* To compile, try:
* mex writeFileNifti.c nifti1_io.c znzlib.c zlib/adler32.c zlib/compress.c zlib/crc32.c zlib/deflate.c zlib/gzio.c zlib/infback.c zlib/inffast.c zlib/inflate.c zlib/inftrees.c zlib/trees.c zlib/zutil.c
* On 32-bit Windows, try:
* ... |
711ae3d3161d9a025154c2542d8f28fd27cd7d1bdf2f6e306e5068dfcdd3f5f6 | C | 10,882 | 343 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
0be1bd4525b7baa431c2384203384074da9aa5f861bbaec7f2fd6036bb1bfea3 | C | 10,890 | 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... |
445af48dcb647995baada0b4ef6ec06659eac653d8d42a058fcd3f6bcfa64eb4 | C | 10,895 | 418 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
3c75e46fc3ed0ad372eb4f34b03e0d6b784d04a79ff7606bbaea6fce1cf0d37f | C | 10,910 | 244 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
1f23dc8382aab65d9286c929893190b68514aa55b8de0366a4a5d4d9a144bc63 | C | 10,982 | 228 | //
// Created by sachetto on 30/09/17.
//
#include "grid.h"
static bool can_derefine(struct cell_node *grid_cell) {
if (grid_cell->cell_data.level > 1) {
if ((grid_cell->next != 0) &&
(grid_cell->next->next != 0) &&
(grid_cell->next->next->next != 0) &&
(g... |
17af6a7a22b00510927f1cf5351beef25375cb801fec42cc5f55b073aa0b2d0d | C | 11,009 | 390 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 Li... |
20f0be7934c23e4a4f7b12b2b65f730ac1f581861f34773f425e08f25cc1369b | C | 11,029 | 402 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
c6dcc4e5a3f3f276e2004cb1dedda01d9ff2923fbcdf843db920c0a760424123 | C | 11,083 | 400 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
c5e68d535e35fa294eb98225f43ff8fcf1c06efd3203b5153b9fc3f5fd757ba7 | C | 11,221 | 523 | /* [email protected] */
/* copyright (C) 2019 */
#include "antisaccades.h"
#include <signal.h>
#define INTSTEPS 8000
double
seria_summary_parameter(
SERIA_SUMMARY_FUNCTION summary_func,
SERIA_PARAMETERS *params)
{
double result;
double ierror;
gsl_integration_workspace *wspace =
... |
a5753c344e13f9d3fbf02966c0ef07badd33a34c7929da0a3ca942005d7a0b0a | C | 11,265 | 275 | #include "lbfgsb.h"
/*
DRIVER 3 in Fortran 77
--------------------------------------------------------------
TIME-CONTROLLED DRIVER FOR L-BFGS-B (version 3.0)
--------------------------------------------------------------
L-BFGS-B is a code for solving large ... |
d2a8488a2edb57909186214b42f0050d8dc8de214963337ec79ce08141d4b67b | C | 11,291 | 522 | #include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include "tisean_cec.h"
typedef double doublereal;
typedef int integer;
#define abs(x) (((x)>=0.0)?(x):-(x))
#define min(x,y) (((x)<=(y))?(x):(y))
#define max(x,y) (((x)>=(y))?(x):(y))
static doublereal c_b10 = 1.;
extern void check_alloc(void*);
double d_si... |
d2efccbb93c2dbe2e59785608fd8d1b5b19b8eab85801e20b519ebcdf32a1600 | C | 11,333 | 316 | /******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
a17c5c3db8c6636ee54d101962b1d1744833e5ce33f3abd6cc7f2d2de784caf0 | C | 11,349 | 368 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
9f1917bf0f49b65dae4442002583875098139c9e29b72ecf73c884d3985823bf | C | 11,385 | 449 | /*Author: Rainer Hegger. Last modified Mar 20, 1999 */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <limits.h>
#include <time.h>
#include "tsa.h"
/* output is written every WHEN seconds */
#define WHEN 120
/* Size of the field for box assisted neighbour searching
(has to be... |
be0c0e916f2026e7999dc5b0660d3fd7695dc5c726975413dfeccaa80db6ed47 | C | 11,390 | 456 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 Li... |
e95b6d49191317a53cfcc2666f8cbe38a2fd61158d267d3437450ad61f801039 | C | 11,404 | 456 | /* [email protected] */
/* copyright (C) 2018 */
#include "mexutils.h"
void
verify_input_theta_array(const mxArray *theta, int dims_theta)
{
int i;
int na = 1;
if ( !mxIsCell(theta) )
{
mexErrMsgIdAndTxt("tapas:sem:input",
"Input parameters should be a cell array");
... |
e1955a3ee10848b678736711a8c4d98df4d004f1474b42d920690b9826f09802 | C | 11,521 | 372 | //========================================================================
// GLFW 3.4 OSMesa - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2016 Google Inc.
// Copyright (c) 2016-2017 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is',... |
2fcaba8e06021cf236ad50deb0144f62b52552ebe0a428f8b1aa7201d949b116 | C | 11,692 | 300 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
3dfc1ac10a1e5dc2a7fd0df316bd3d528409c2981d3a2bce603993c7d93c87cd | C | 11,693 | 436 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
a5bebebc345c45ab225ade577c807cde2b55acb0de4affd617d20d0f11cd8a2b | C | 11,716 | 363 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
0457f3bd85a8469912e081e55d77aa76179a3364ee07b9b3ce9286fac43ec67e | C | 11,752 | 482 | #include <assert.h>
#include <stdlib.h>
#include "ten_tusscher_2004.h"
GET_CELL_MODEL_DATA(init_cell_model_data) {
assert(cell_model);
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_... |
f18658042c918c57088ad39645b59b97d830138fc7ba43f72ef183101d038536 | C | 11,752 | 332 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2018 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is... |
7dd3d5fee9afe86c77135373fa73bf4e1ee80f8d1ab6b19366c9c08d87508be7 | C | 11,760 | 442 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
1b850dfde5d57314db5f5c0816dab546f94ac6fd7393551d0be8db1ecb4f1f6f | C | 11,785 | 482 | //Original Ten Tusscher
#include <assert.h>
#include <stdlib.h>
#include "ten_tusscher_2004_epi.h"
GET_CELL_MODEL_DATA(init_cell_model_data) {
assert(cell_model);
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITI... |
74b41b74bd3bdb1ce51f4432deb97e30058539d120dd8db07c503043fe363328 | C | 11,811 | 348 | /*=================================================================
*
* lbfgsb_wrapper.c, mex gatewate interface
* You can call this directly from Matlab,
* but I strongly suggest using lbfgsb.m, since many
* variables are modified in-place, and lbfgsb.m will
* handle them correctly. It also shows you how to use
... |
157fddd6e2b0c3028aaea8d99a3cb6786be4a5e41fd2b9ca695f65d4612c7f42 | C | 11,851 | 377 | /****************************************************************
**
** Set of routines implementing a 2D or 3D connected component
** labelling algorithm. Its interface is modelled on bwlabel
** (which is a routine in the image processing toolbox) and
** takes as input a binary image and (optionally) a connectedn... |
024127e4ce17811a356a9928527ebcdcb209c4f2119a627b0916821c3c135c6f | C | 11,858 | 485 | /*
* lat_ops.c - benchmark of simple operations
*
* Copyright (c) 1996-2004 Carl Staelin and Larry McVoy.
*
* This benchmark is meant to benchmark raw arithmetic operation
* latency for various operations on various datatypes. Obviously,
* not all operations make sense for all datatypes (e.g., modulus
* on f... |
8fa2a29e789b3df2cccbec990bd794d642951a3d209ed442d7c0dddb6cfbb29e | C | 11,863 | 379 | //
// Created by sachetto on 02/10/17.
//
#include "ode_solver.h"
#include <assert.h>
#include <dlfcn.h>
#include <string.h>
#ifdef COMPILE_CUDA
#include "../gpu_utils/gpu_utils.h"
#endif
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../config_helpers/config_helpers.h"
struct ode_solver ... |
6ee25acb881d745960a775dc2e30211e4b33347a049f40ccaa99404809345469 | C | 11,874 | 410 | /*
* @file
*
* A C shim library to assist in interfacing to Spinnaker with
* Python. This primarily handles spinImageEvent callbacks
* which enable us to take continuous movies instead of grabbing
* a series of random images.
*
* Compile using scons and storm-control/SConstruct.
*
* $ cd storm-control
* $ p... |
18d6638f6b50b3abcb5e7f4de9623c5f86673bb60ea50e3f77a58395827ef321 | C | 11,909 | 192 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
a1ba209a190dd77842a166ac8b8c8c2e3272bfbe7e5afa63d50b869179467052 | C | 11,973 | 603 | #include <math.h>
#include "bench.h"
#define BOOTSTRAP_COUNT 200
/*
* a comparison function used by qsort
*/
int
int_compare(const void *a, const void *b)
{
if (*(int*)a < *(int*)b) return -1;
if (*(int*)a > *(int*)b) return 1;
return 0;
}
/*
* a comparison function used by qsort
*/
int
uint64_compare(const v... |
afe6cf9c09efc2ce15320d159918345b93050fe42dcc3ee50315ed580e669ba0 | C | 12,028 | 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"), ... |
90556d5ed6063e59b723eeff2cdc88afeecf5fd52d3e61eb092c1960d12fcf00 | C | 12,037 | 445 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
1a8d5e34f67bb64ec201bcb7f4eeda67786df6f5aacfe0e0802e4a9fb4f1d6ef | C | 12,071 | 428 | /* stbmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
89b972d0a3fa3536a6d440d53a61ec0b2056bdb9feb835f8e26267b89228a8e5 | C | 12,085 | 428 | /* dtbmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
6ec58f2e6f59896ef00ec5a311c0f7fdfcfd0ec243cd685a6ae8853adb5a2cb7 | C | 12,090 | 271 | #include"build.h"
/*void open_files()
{
p[0] = fopen("output/I_CaL.dat","w");
p[1] = fopen("output/I_Na.dat","w");
p[2] = fopen("output/I_K1.dat","w");
p[3] = fopen("output/I_Kr.dat","w");
p[4] = fopen("output/I_Ks.dat","w");
p[5] = fopen("output/I_Kto.dat","w");
p[6] = fopen("output/I_Kpl.dat","w");
p[7] = f... |
abd788865138556947c7a48f3d17dedfed65f623983aacfc2c1c37463a44faf3 | C | 12,106 | 441 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
83714280d9aea156252b7cfdff85e3de735444237931622bcde352abed079439 | C | 12,155 | 437 | /* file flann_example.c */
// #define FLANN_USE_CUDA
#include "exception.h"
#include "q6q6_cmdline.h"
#include "string.h"
#include <assert.h>
#include <complex.h>
#include <flann/flann.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
/**
* @brief swap float value to big endian
*
* Paraview's vtk forma... |
784e4a6c7af31e3f80c94e7c33b3a0803c9e85c4f99bf028670f368fa088be3e | C | 12,169 | 455 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
860b02e5afc48afab6cdfce2ecc063baa0cbe580ad480819422d5eef5355a1e1 | C | 12,266 | 415 | /*==========================================================
* sampen_mex.c -
*
* Converted to mex file for Matlab by Ben Fulcher
*
* This is a MEX-file for MATLAB.
*
*==========================================================
file: sampen.c Doug Lake 2 August 2002
Last revised: 1 November 2004 (by george@m... |
7c9b2fbc890e2f0d92dd5513a7020985320ac5037766caf0a57c773972228e03 | C | 12,306 | 454 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
db78970ec6e6a9fc1fdb1af70e95437d641c5beec41c179898aa7e71e4dc654b | C | 12,339 | 428 | //========================================================================
// GLFW 3.4 Linux - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2017 Camilla Löwy <[email protected]>
//
// This software is provided ... |
32f52e11f6b871942daf635004d750a41b71b8257953ca36112fd1647df0b675 | C | 12,375 | 443 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
bc4ccbe8b726a8566577e8715c3fa405288818b4439ec3939273210ae79252ec | C | 12,413 | 454 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
eb6e5b358feb6b7083483bda90307b2c00286570b98ffc34da86abea87e91155 | C | 12,416 | 459 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
b9fc1510e338d6d717d6208d29d773ee3451f86c5923d582903ebe02ec95ff5d | C | 12,453 | 490 | /* file: sampen.c Doug Lake 2 August 2002
Last revised: 1 November 2004 (by [email protected]) 1.2
-------------------------------------------------------------------------------
sampen: calculate Sample Entropy
Copyright (C) 2002-2004 Doug Lake
This program is free software; you can redistribute it and/or modify it u... |
7a5547370cfa9502d92962813c4300a9ac224d0e2c104ce1cdead6c316a65d27 | C | 12,458 | 448 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
3ad137011d5597b3357def0a57074aab75a27039cee1b0e6083c61ecf0b5bc0e | C | 12,469 | 459 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
5005ba4a46a9665b477b3114413b216ff9b7483d1ef0a54ba6e38f8cf21d8397 | C | 12,487 | 624 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
f8b22a79e30944bce869837cd966e59c8a73e99eab805e2f64b82afec84cbc65 | C | 12,508 | 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... |
464751a3991d5a70112a2fa548ae00141ecaaa9201d6b3ef38e53c9c00b0ffc4 | C | 12,538 | 276 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
7ef349bc42b9e629a2417612bd664d63fdd5421bccc4f126adcde73d008493ab | C | 12,567 | 462 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 Li... |
1cdc2db0625e0b680f1b39f4752667f40ac3f9c66d743b67e3f96244ca31f2dc | C | 12,724 | 388 | //
// Created by bergolho on 19/07/18.
//
#include "purkinje_helpers.h"
#include "../libraries_common/common_data_structures.h"
#include "../logger/logger.h"
#include "../utils/utils.h"
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include <math.h>
#include <string.h>
// Set a a custom Purkinje ne... |
d0df3f2028364542b8f26be57e1ac8259043bd36ba7aa2fc5783b43da50bf305 | C | 12,760 | 466 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
4d7ed8ab92d1696cbc33e9370e787813958d9bd1c71f762f00ae9c4a347f3e3b | C | 12,768 | 434 | /**
* @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... |
8237e05b23ff7ad3e9410b6bd77da2675f03b684ee9755367a446a78dfc9288d | C | 12,784 | 466 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
1e46704beacfc7b5a83c12a124b991b5517a9c78e86aac8058ca3c6f3a623fe1 | C | 12,818 | 378 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
78e4dfa331ebf35e17681ba873640abee76696036c3a1a011aea81cd6f6a8582 | C | 12,854 | 409 | /******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
63fa5d277aaefbf583e96f9616260aa5739762787889101463c43892d10257a0 | C | 12,863 | 469 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if !NRNGPU
#undef exp
#d... |
0b350bed6314ffe6734456146c7951daa09d1befd7fe8de67533feb928646e0e | C | 12,867 | 368 | #include <stdint.h>
#include <string.h>
#include <stdio.h>
#include <assert.h>
#include "mmpriv.h"
#include "kalloc.h"
#include "krmq.h"
static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
{
int64_t i = z[k].y, end_i = -1, max_i = i;
int32_t m... |
a9fd40871e1b10424fa2a325d2d8aec21ca1afc98dc2e56f4c0c98cb333edcb7 | C | 12,877 | 419 | /******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
df0901057b6b49c34c7ed6535de91642efe17ac32946b08133f3c6098ca68145 | C | 12,890 | 318 | ////
//// Created by sachetto on 06/10/17.
////
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../utils/file_utils.h"
#include "common.h"
#include <criterion/criterion.h>
static int check_ecg_file_equals(sds gold_ecg, sds tested_ecg, float tol) {
string_array lines_gold = read_lines(gold... |
2e0d17aa20c71c3db4ee6097196b59709f08732732c7242cf8a333c9ff9f2050 | C | 12,983 | 460 | /*
* @file
*
* Perform various manipulations on sCMOS image data. This is written
* in C for performance reasons.
*
* Hazen 10/13
*
* Add additional functions to cover all the orientation possibilities.
*
* Hazen 09/15
*
*
* Compilation (windows):
* gcc -c c_image_manipulation.c -O3
* gcc ... |
b7997132bebb4253092330a8e99a28c9aa4981e703e2496e75f9ba5ad3723cc7 | C | 13,104 | 503 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 Li... |
237cc0adf0da2b084a6bd1f9931cdf50d391bd05260a1de8e5fee9a35fe97f5c | C | 13,133 | 447 | // peaks. Copyright (c) 2020. Winfield Chen.
#include <stddef.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <stdio.h>
#include "format.h"
#include "maps.h"
char const * format_t(int const t) {
static char const * const map[256] = {
[0] = "%*s",
... |
09ad6206f03397d1c2de532990307764683cb7dc8b6c099e630ccc11ebcf6b71 | C | 13,232 | 436 | /*
* @file
*
* Object finding code based on using the median background
* subtraction and threshold object detection.
*
* Hazen 3/09
*
* Linux:
* gcc -fPIC -g -c -Wall MedianCounter.c
* gcc -shared -Wl,-soname,MedianCounter.so.1 -o MedianCounter.so.1.0.1 MedianCounter.o -lc
*
* Windows:
* gcc -c Medi... |
09116aae1c39963e101f3b99a743ffc9422a2f372bb0b722bf77b57de47da40e | C | 13,235 | 305 | #include <string.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#include <emmintrin.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
#endif
#ifdef KSW_CPU_DISPATCH
#ifdef __SSE4_1__
void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint... |
a05584c5e3a8f457c8fc203a297291eb4bae76c8be313bc41e97330a9081728b | C | 13,339 | 311 | #include <string.h>
#include <assert.h>
#include "align-ksw2.H"
#ifdef __SSE2__
#include <emmintrin.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
#endif
namespace merylutil::inline align::inline ksw2::inline v1 {
#ifdef KSW_CPU_DISPATCH
#ifdef __SSE4_1__
void ksw_extz2_s... |
74c491c834396b574df1246beb27186118e4e7a2d3373b66134b713998409f7d | C | 13,354 | 313 | #include <string.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#ifdef USE_SIMDE
#include <simde/x86/sse2.h>
#else
#include <emmintrin.h>
#endif
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#ifdef USE_SIMDE
#include <simde/x86/sse4.1.h>
#else
#include <smmintrin.h>
#endif
#endif
#ifdef ... |
e12606fb1d83eb7c3898b23d4fab48aa6e09e592dcc8607f247dfd6be476a85a | C | 13,426 | 486 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 Li... |
ed4ffc0866ba6a4020c21340fef04571efd334e45cc1dfaa6890f6aa12319231 | C | 13,464 | 438 | /* chpmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
68d772c62decce63688e6b634af31b3eae1c822cc873f82a3ec1d18834163bcc | C | 13,498 | 438 | /* zhpmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
75422357957163e5f13b569cc1e5bfae235c3cf6b3263459293ff7e82e564de2 | C | 13,611 | 411 | /*******************************************************************
Copyright (C) 2001-2012 Leo Breiman, Adele Cutler and Merck & Co., Inc.
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 R_Free Software Foundati... |
fd8acc563c638037fa727a7f3dd3e5bb304abe0f3583ec08cc24eea66bf46aac | C | 13,634 | 501 | /*
* par_ops.c - benchmark of simple operation parallelism
*
* Copyright (c) 2000 Carl Staelin.
* Copyright (c) 1994 Larry McVoy. Distributed under the FSF GPL with
* additional restriction that results may published only if
* (1) the benchmark is unmodified, and
* (2) the version in the sccsid below is include... |
a437be03e0adb1c2d3f6089d7044c860704bd9e0ebeee04980ddf5ab3b6d6de8 | C | 13,734 | 402 | /*******************************************************************
Copyright (C) 2001-7 Leo Breiman, Adele Cutler and Merck & Co., Inc.
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 R_Free Software Foundation;... |
e503c3ea5ea2d81aa58cc0f7e22067722f7f7aaa4cafd1224e34d185432faafe | C | 13,750 | 551 | /*
* bw_mem64p.c - simple memory write bandwidth benchmark with various read:write proportion
*
* Usage: bw_mem64p [-P <parallelism>] [-W <warmup>] [-N <repetitions>] size what
* what: rw21 rw31 rw41 rw51
*
* Copyright (c) 2025 Huang Ying
*
* Distributed under the FSF GPL with additional restriction that... |
9ee0ad97a119ae2461102ccf0c1d4d3962e64e6cacd3d513786da8c46044ca04 | C | 13,790 | 334 | /* L-BFGS-B is released under the "New BSD License" (aka "Modified BSD License" */
/* or "3-clause license") */
/* Please read attached file License.txt */
#include "lbfgsb.h"
/*
DRIVER 1 in Fortran 77
--------------------------------------------------------------
SI... |
155c7e9f39974ec34c7c07a330f202342c33134047c00dd25192bdfb6c85bb3f | C | 13,804 | 462 | //
// Created by bergolho on 25/01/19.
//
#include "vtk_polydata_grid.h"
#include "data_utils.h"
#include <stdint.h>
#include "../3dparty/stb_ds.h"
#include "../logger/logger.h"
struct vtk_polydata_grid *new_vtk_polydata_grid ()
{
struct vtk_polydata_grid *grid = (struct vtk_polydata_grid *)malloc(sizeof(struct ... |
b063efa861980f4c75e1f72150c32fa31337db123efb8679b45906f33d212432 | C | 13,831 | 476 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
f7d2748acfe3ae4e2d81e2ff25828849d3bf1e4d1383b936dcce01fa7126005b | C | 13,907 | 407 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
baba23f8170eb1efe36327b4c6eea15d1e95a4009b7bb61dbfbfe0b22276e3fb | C | 14,028 | 438 | /*
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... |
e5c6d687f99c240e5f9d2303288df60cc21c73669eb1883d8b54c8d3884b6f68 | C | 14,213 | 507 | /*
* mhz.c - calculate clock rate and megahertz
*
* Usage: mhz [-c]
*
*******************************************************************
*
* Caveat emptor and other warnings
*
* This code must be compiled using the optimizer! If you don't
* compile this using the optimizer, then many compilers don't
* make... |
53028f61b419d55387f2a871713b314204cec9ffbd916c3c74116d45fc7036ef | C | 14,441 | 574 | /* [email protected] */
/* copyright (C) 2017 */
#include "antisaccades.h"
// This is done to reparametrize the code inside c as opposed to matlab
const ACCUMULATOR ACCUMULATOR_INVGAMMA = {
.pdf = invgamma_pdf,
.lpdf = invgamma_lpdf,
.cdf = invgamma_cdf,
.lcdf = invgamma_lcdf,
.sf = invgamm... |
ca94bc61178e1899eec6f72fde9be6a1c9f3aac422f5e886561022b924784bc7 | C | 14,555 | 427 | /*******************************************************************
Copyright (C) 2001-2015 Leo Breiman, Adele Cutler and Merck & Co., Inc.
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 R_Free Software Foundati... |
76d3501363202317bda7937bbfda30b10a7c0c046a79a692db5ce4fe3f5d868c | C | 14,826 | 534 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
a3775529c0d8fe14894fe6aa57144782a92f716a37144564175bbce1dd6f39fc | C | 14,828 | 468 | /* pliocomp.c */
/*
Copyright (Unpublished--all rights reserved under the copyright laws of
the United States), U.S. Government as represented by the Administrator
of the National Aeronautics and Space Administration. No copyright is
claimed in the United States under Title 17, U.S. Code.
Permission to free... |
2e886aec7d7a5638a06a28a7c932dd4992d9c24af3df6f47f0a413ee63a22e43 | C | 14,847 | 504 | /*
* bw_mem.c - simple memory write bandwidth benchmark
*
* Usage: bw_mem [-P <parallelism>] [-W <warmup>] [-N <repetitions>] size what
* what: rd wr rdwr cp fwr frd fcp bzero bcopy
*
* Copyright (c) 1994-1996 Larry McVoy. Distributed under the FSF GPL with
* additional restriction that results may publi... |
680c923f5b208ad56c3e2d6b0f5f07f1a03a9dd604c83d8da756063d983760b4 | C | 14,979 | 542 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is... |
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