sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b7759d0bf45db5dcfa014da63a004dbd97992a51499859e7042dbbe054294acb | C | 5,353 | 167 | //
// Created by sachetto on 07/04/2020.
//
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../logger/logger.h"
#include "../utils/stop_watch.h"
#include "common.h"
#include <gdbm.h>
struct elapsed_times {
double config_time;
double simulation_time;
double total_time;
} __attribut... |
5f8fa2883b3fbcafac97c309c5e99dc47094c210307392a303647fc12ed2a876 | C | 5,363 | 169 | #include <zlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#define __STDC_LIMIT_MACROS
#include "bseq.h"
#include "kvec.h"
#include "kseq.h"
KSEQ_INIT2(, gzFile, gzread)
unsigned char seq_comp_table[256] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, ... |
9e8f1994e7d2d9c755cbb38c322880c12babd17f4a93356976990c70841dcf8d | C | 5,365 | 173 | /*
* 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... |
efd7e36993831181a8d96e3b88983a2b0375fbbcfc7eb4311bee2bafd6491444 | C | 5,371 | 190 | /*
* 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... |
10cc964ce61f5d83684aac9c526263a05a7c7bfd6a668eb427804469acbdf850 | C | 5,392 | 185 | /*
* 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... |
aae4d84e3fc0bd56287d378b4c7bf41b27f300a89c06a97cf788bc4b394e8a20 | C | 5,437 | 157 |
/******************************************************************************
*
* 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://... |
b9d573db0af6816d7f21f0ab57238719ea180525f863a8808cf64c803a3a6a60 | C | 5,473 | 216 |
/******************************************************************************
*
* 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://... |
72e97efdc506fd711dd5ed811cb1a734d3b077478e16d42547634346a6313031 | C | 5,550 | 196 |
/******************************************************************************
*
* 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:
* ... |
0357db604c8a6efd68776c2fc5c22f630ba83374cc4191749ca227f0e75eb715 | C | 5,585 | 190 | /* vcf_sweep.c -- forward/reverse sweep API.
Copyright (C) 2013-2014, 2019 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 w... |
c04f0309258d6da1363d69ccffae2207d47b9a9668806d0b72fb9745e4f46c7f | C | 5,589 | 227 | #include "types.H"
#include "files.H"
#include "system.H"
#include "math.H"
#include <vector>
class cpBuf {
public:
cpBuf(FILE *F, uint32 max) {
_b = new uint8 [max];
_bLen = merylutil::loadFromFile(_b, "stuff", max, F, false);
}
~cpBuf() {
delete [] _b;
}
uint32 _bLen = 0;
uint8 *_b ... |
889704b3771d38c97a3d9df4e73cc8f0b1faafff4e7ad6ba18bf851d1ecefbcb | C | 5,608 | 231 | /*Author: Rainer Hegger Last modified: Sep 4, 1999 */
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <limits.h>
#include "routines/tsa.h"
#define WID_STR "Performs a global SVD"
unsigned long LENGTH=ULONG_MAX,exclude=0;
unsigned int DIM=2,LDIM=2,COLUMN=1,DELAY=1;
unsigned int ve... |
ef8971c80a4d5be9d1b59cf2bcd00018f722d613363d3cffa2c2dc38b80b78d1 | C | 5,622 | 226 | /*=================================================================
*
* SHANNON.C .MEX file corresponding to SHANNON.M
* returns the approximate Shannon Entropy, for a n-bin
* encoding of the time series x at depth d
* I.e. -\sum Plog(P)
* where P=(x_i,x_{i+1... |
65c21db36ef31f1dfce04eb98e9ccf17b6e793185bbae6129e34bcb9276b4b34 | C | 5,697 | 177 | #include <stdlib.h>
#include <math.h>
#include "mmpriv.h"
#include "kvec.h"
void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0;
... |
e52e24244f93ab57be8806c9480a42c3d61e0259f01d5e3214b35951726f9b67 | C | 5,724 | 222 | /***************************************************************************/
/* */
/* Program: tools.C */
/* Version: 2.0 */
/* By: ... |
eec7dd9160f7bba6cb1f0991f6772c064a0423a4fa152ab26683c60d6bd86a3e | C | 5,728 | 197 | /* Close returns code by M. Little (c) 2006 */
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include "mex.h"
#include "matrix.h"
/* Real variable type */
#define REAL double
/* Input parameters */
#define X_IN prhs[0]
#define EMBEDDIM_IN prhs[1]
#define EMBEDDEL_IN prhs[2]
... |
c2fa6ebca85a7ac8a8e592b45bdc561bd2b5fb4ecf0f474e9e05a7f8a45079e6 | C | 5,795 | 206 | /*
* 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... |
16e7e5bd140bbf7fc88057ee0c354138f1e7447ec275c8a8d083560fe0fb0199 | C | 5,800 | 167 | #include <stdint.h>
#include <string.h>
#include <stdio.h>
#include "minimap.h"
#include "mmpriv.h"
#include "kalloc.h"
static const char LogTable256[256] = {
#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
LT(4), LT(5), LT(5), LT(6), LT(6), LT(6), LT(6),... |
5253efbfb70f00fe22039470f44fd553bc30fdaa443965e1a05d122a622649cb | C | 5,812 | 229 | #include "graph.h"
struct graph* new_graph () {
struct graph *result = MALLOC_ONE_TYPE(struct graph);
result->last_node = NULL;
result->list_nodes = NULL;
result->total_nodes = 0;
result->total_edges = 0;
result->has_point_data = false;
return result;
}
void free_list_edges (struct node *... |
a6afcbacc171bdac1a2b3720c13e01c239b3052b94fb82b441e27d622eab4bc8 | C | 5,814 | 182 | #include <stdlib.h>
#include <math.h>
#include "mmpriv.h"
#include "kvec.h"
void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0;
... |
475fb2d974267aa3436acfd144f1639267ee8d349530c7df3e36a051f727e6e8 | C | 5,824 | 231 |
/******************************************************************************
*
* 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:
* ... |
9cd8c6b348b3ce166897c883a2a4bfdde58c9df925430c47ce539d685a611b99 | C | 5,829 | 143 | #include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#define __STDC_LIMIT_MACROS
#include "kvec.h"
#include "mmpriv.h"
unsigned char seq_nt4_table[256] = {
0, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, ... |
04f190b29113f467c9e37f1463ce0cbc961a123f0052204510e3897a95c9ad66 | C | 5,865 | 269 |
/******************************************************************************
*
* 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:
* ... |
493789f107b06d3898baaf1b1d64f476a84abd627d373669350310dfe059ee93 | C | 5,900 | 163 | #include "sparseinv.h"
/* sparsinv: computes the sparse inverse subset, using Takahashi's equations.
On input, the pattern of Z must be equal to the symbolic Cholesky
factorization of A+A', where A=(L+I)*(U+I). The pattern of L+U must be a
subset of Z. Z must have zero-free diagonal. These conditions are
... |
94e028138991a3c6304ea079bca5879d31740206c39cbe683232942b0de2b74e | C | 5,932 | 238 | /*
* lat_mem_rd.c - measure memory load latency
*
* usage: lat_mem_rd [-P <parallelism>] [-W <warmup>] [-N <repetitions>]
* [-s <start>] [-e <end>] [-c <count-limit>]
* [-t [-p <chase-page-size>]] size-in-MB [stride ...]
*
* Copyright (c) 1994 Larry McVoy.
* Copyright (c) 2... |
e0873713bfef4b519a223980e72fa8ed48821d65225af4be44859baec5b4e1c4 | C | 5,938 | 219 |
/******************************************************************************
*
* 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:
* ... |
b1db0ee9038ef2051bb6357342ab4a6d28975f287938bcaa05aa568cc059d98c | C | 5,982 | 207 |
/******************************************************************************
*
* 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:
* ... |
b690760d362b18eba370d18d41b22519ae9c8f5c1d442de9d2013900d1713d27 | C | 5,985 | 172 |
/******************************************************************************
*
* 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://... |
9523ed0597aa5a4b4ac53f443f525ffa1c58923da3ee2f23024b66a428229478 | C | 6,027 | 164 | #include "3dparty/ini_parser/ini.h"
#include "3dparty/stb_ds.h"
#include "alg/cell/cell.h"
#include "alg/grid/grid.h"
#include "config/config_parser.h"
#include "config/domain_config.h"
#include "eikonal/eikonal_solver.h"
#include "config/stim_config.h"
#include "logger/logger.h"
#include "utils/file_utils.h"
#include ... |
e0472cffcedca799cc31d98d23862bd016a77e5e68208d7e236c2cda24a05962 | C | 6,087 | 184 | /*
* Copyright (c) 2000-2010 Marc Alexander Lehmann <[email protected]>
*
* Redistribution and use in source and binary forms, with or without modifica-
* tion, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
18447586bba49bf090722a6b69fc0985d11e15e777efc0719afa6af48dd2b2e9 | C | 6,097 | 200 | #include"build.h"
void allocate_arrays()
{
I_app1 = allocate_1d_array(mypoints+2);
I_app2 = allocate_1d_array(mypoints+2);
CaMCa = allocate_1d_array(mypoints+2);
TnChCa = allocate_1d_array(mypoints+2);
SRCa = allocate_1d_array(mypoints+2);
p_O_NaT = allocate_1d_array(mypoints+2);
p_I_2... |
33ceff673d8e30b8f2102b594259edbbf5e0db0d4b3b114edf5922dea4bebaf8 | C | 6,101 | 203 | /* Matlab MEX implementation of Kalafut-Visscher step-finding algorithm.
Usage:
Input:
x - Input signal: must be a row vector
Output:
intervals - List of step points: zeros should be ignored
(c) Max Little, 2010. Adapted from code written by B. Kalafut et al.
The algorithm is describ... |
a7718b552fb6313aee71c1b464c07f634376cb5a809336169f4a7a8bc8563fb3 | C | 6,103 | 225 | /*
* 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... |
528e09120bb053f5d153c3d938ff1e9298c2762ce12d139c10813b1edd86d8f4 | C | 6,151 | 272 | /*
* Benchmark creates & deletes.
*/
char *id = "$Id$\n";
#include "bench.h"
struct _state {
char *tmpdir;
int max;
int n;
char** names;
int ndirs;
char** dirs;
size_t size;
};
void measure(size_t size,
int parallel, int warmup, int repetitions, void* cookie);
void mkfile(char* s, size_t size);
void set... |
71a4facfaa198ab5e17725d186a574ae03d4d976f0bff1dde47a20e1fb430515 | C | 6,168 | 212 | // peaks. Copyright (c) 2020. Winfield Chen.
#include <stdint.h>
#include <stdlib.h>
#include <stdio.h>
#include <errno.h>
#include "heap.h"
#include "format.h"
struct heap heaps[23] = {
[0].chr = 0,
[1].chr = 1,
[2].chr = 2,
[3].chr = 3,
[4].chr = 4,
[5].chr = 5,
... |
98914cc9b3c69a0d9164108b609c22df7dd72ff4df368f0ed5153ef114fb2c18 | C | 6,172 | 281 | /*
* lat_rpc.c - simple RPC transaction latency test
*
* Four programs in one -
* server usage: lat_rpc -s
* client usage: lat_rpc hostname
* client usage: lat_rpc -p tcp hostname
* client usage: lat_rpc -p udp hostname
* shutdown: lat_rpc -S hostname
*
* Copyright (c) 2000 Carl Staelin.
* Copyright (c) 1994... |
3bb750a8e089421c1e3e479b1549c9bbfcf6715b2b51f79469400c75c49c1adf | C | 6,195 | 235 | #include "build.h"
void main(int argc,char *argv[]){
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&numProcs);
MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
// starttime = MPI_Wtime();
/*********** NUMBER OF INTERIOR GRID POINTS ALLOCATED TO EACH PROCESSOR ************/
mypoints = x_sp... |
f60ea731917242d122f21da8b2afb59d73ff2148b3cfa2908721aa41b08ef0e6 | C | 6,237 | 249 | #define EXTERN
#include"variables.h"
#include"constants.h"
#include<stdio.h>
#include<math.h>
#include<mpi.h>
int main(int argc, char** argv)
{
/*-----Initializing the MPI environment -----*/
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&num_procs);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
rank1 = 6;
ra... |
9202f432a783131eaac900098e77551e0be3e2915efa5bdd57e3cba680218c06 | C | 6,250 | 279 | /* bits - handle operations on arrays of bits.
*
* This file is copyright 2002 Jim Kent, but license is hereby
* granted for all use - public, private or commercial. */
#include "common.h"
#include "bits.h"
static char const rcsid[] = "$Id: bits.c,v 1.20 2008/03/25 16:32:31 angie Exp $";
static Bits oneBit[8] =... |
51436a6f6ff24f692a20657c5a1eb61c4b1ca27b1765ebf06b72f00b6206c153 | C | 6,257 | 259 | /*
* lat_usleep.c - usleep duration/latency
*
* The APIs for usleep(3), nanosleep(2), select(2), pselect(2),
* getitimer(2) and setitimer(2) support resolutions down to
* a micro-second. However, many implementations do not support
* such resolution. Most current implementations (as of Fall
* 2002) simply p... |
4fbe40c157c5485001715d096d50208f77e2b11cd31ac65f0f404da673127f73 | C | 6,262 | 205 |
/******************************************************************************
*
* 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:
* ... |
2f4114f51ba258005faabec07ab48ccc9ef69e5c40cd87bbd2cf70b4fefb16fb | C | 6,275 | 212 |
/******************************************************************************
*
* 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:
* ... |
d0604a560dd0fec06365db7df777fa4a89c7e473623194fea16568adc4a51c79 | C | 6,324 | 240 | #include "bench.h"
/* #define _DEBUG */
#if defined(HAVE_SYSMP)
#include <sys/sysmp.h>
#include <sys/sysinfo.h>
#endif
#if defined(HAVE_MPCTL)
#include <sys/mpctl.h>
#endif
#if defined(HAVE_BINDPROCESSOR)
#include <sys/processor.h>
#endif
#if defined(HAVE_PROCESSOR_BIND)
#include <sys/types.h>
#include <sys/proces... |
2ae706559081dff13198d24b70822cf68a800f339847e9014376061702d276ca | C | 6,325 | 225 | /*
* 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... |
34dfe3502afc3afd97da3c2e53024fc303b41c637ce53618597562f0820f0951 | C | 6,348 | 88 | #include "build.h"
void CaRU() {
p_O_RyR = Y_ooo[ii] + Y_coo[ii] + Y_cco[ii] + Y_oco[ii];
p_O_RyR_t = ((1))*p_O_RyR + p_O_RyR_base;
J_Ca_rel = ((1))*P_RyR * p_O_RyR_t * (Ca_2_SRrl - Ca_2_jnc[ii]) * Sc_Cell;
Ca_2_nd_00 = Ca_2_jnc[ii];
Ca_2_nd_L0[ii] = (Ca_2_nd_00 + f_L * delta_RTF * Vm[ii] * exp(-delta_RTF * Vm... |
e6f8baddf67a585a8a6051b397d3ffec0c52bec9a223e2e28e1a7ab11366c60f | C | 6,351 | 295 | /* srotmg.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 e... |
ec8595375979eef14872465cb059004235f6374c36b18d3f0e2c06bec71f91fe | C | 6,356 | 187 | // Author: Lucas Berg (@bergolho)
// Script used to clip a section of a mesh and extract the extra data information
// Version: 29/01/2024
// Last change: 29/01/2024
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include "3dparty/stb_ds.h"
#include "common_types/common_types.h"
#inclu... |
840d751cbd31e0c17f857cc96a36550928cbae6cf0168a3d95cb0871b53bf2e0 | C | 6,462 | 303 | /*
* disk - calculate zone bandwidths and seek times
*
* Usage: disk device
*
* Copyright (c) 1994-1997 Larry McVoy. All rights reserved.
* Bits of this are derived from work by Ethan Solomita.
*/
#include <stdio.h>
#include <sys/types.h>
#include <unistd.h>
#include <stdlib.h>
#include "bench.h"
#include "flu... |
41d79b64927e7a74fbf42e3cc23947a8631f88c8c2ad5a53e20be05526c070a6 | C | 6,486 | 293 | /* drotmg.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 e... |
4fe83ac596f259b15bf0cf8a0f6d407f62833efa303c87e0f1f9c463a86c0d92 | C | 6,512 | 244 | /* inih -- simple .INI file parser
inih is released under the New BSD license (see LICENSE.txt). Go to the project
home page for more info:
https://github.com/benhoyt/inih
*/
#if defined(_MSC_VER) && !defined(_CRT_SECURE_NO_WARNINGS)
#define _CRT_SECURE_NO_WARNINGS
#endif
#include <stdio.h>
#include <ctype.h>
#inc... |
5a6b9f862c24fe380f49bea205e1f15551e7a4328ca7bc7d1005243bab8c0547 | C | 6,515 | 241 | /*
* 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... |
563bab19114a25339afc1251b93899be16b194e77f2e4c911508c06e76a1317d | C | 6,529 | 271 |
/******************************************************************************
*
* 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://... |
d6ce38ae08ea32f7f7f826d3269bdcde13223e0c48a9ec9e9403dda50fc62fa0 | C | 6,544 | 252 | /*
* 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... |
078ec1d3ab3f6565e5186fbbaacb7cf5681aa84f3252fe632c0a5585d4d46db8 | C | 6,593 | 212 | #include"variables.h"
#include"constants.c"
void currents()
{
/* INa: Fast Na+ current (inward) */
I_Na=G_Na*pow(m,3)*h*j*(V-E_Na);
m_inf=1/pow((1+exp((-56.86-V)/9.03)),2);
alpha_m=1/(1+exp((-60-V)/5));
beta_m=0.1/(1+exp((V+35)/5)) + 0.1/(1+exp((V-50)/200));
tau_m=alpha... |
5bcb3722102a75e83b728c17e9d06fdbee27bcf83d2a8cb743a40993c7038c27 | C | 6,602 | 212 | #include <mpi.h>
#include <stdlib.h>
#include <string.h>
#include "3dparty/ini_parser/ini.h"
#include "3dparty/ini_parser/ini_file_sections.h"
#include "3dparty/sds/sds.h"
#include "3dparty/stb_ds.h"
#include "alg/grid/grid.h"
#include "config_helpers/config_helpers.h"
#include "logger/logger.h"
#include "monodomain/m... |
95e89f89228e7935b97322bd6d07f39d6e17359c1e4aca5f499dd24751774777 | C | 6,611 | 242 | /*
* 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... |
ee5dc68ae3dd51722091704dc1e2c0d28da2ed45e91976b530dbf227a204fbc2 | C | 6,612 | 185 | #include <assert.h>
#include <stdlib.h>
#include <math.h>
#include "minimal_model.h"
#include <stdio.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_INI... |
024b1b746b1b3f8ca8cffe6ce6589e9c5569264fda5160e5210442d8ae6a6fd0 | C | 6,642 | 213 | #include <string.h>
#include <stdint.h>
#include <stdio.h>
#include "kalloc.h"
#include "kdq.h"
#include "kvec.h"
#include "sdust.h"
#define SD_WLEN 3
#define SD_WTOT (1<<(SD_WLEN<<1))
#define SD_WMSK (SD_WTOT - 1)
typedef struct {
int start, finish;
int r, l;
} perf_intv_t;
typedef kvec_t(perf_intv_t) perf_intv_v... |
3f44ee99700389849a4b06967b0c8d06ea3a1613f9662afdf52e9e67af94fc8d | C | 6,703 | 303 | /*
* Copyright (c) 2014, Volkan Yazıcı <[email protected]>
* 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... |
bb936c7b11a6c26e8ff64cb8da15937a41d764889aadb3c502d0eb0eae88e976 | C | 6,776 | 208 | /* errmod.c -- revised MAQ error model.
Copyright (C) 2010 Broad Institute.
Copyright (C) 2012, 2013, 2016-2017, 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 (... |
e5cca45392b601b09a7c340e800225c4ed44205e7ab5bd3ac5155ba6c6d08802 | C | 6,801 | 207 | /*
* Copyright (c) 2019-2021 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,
* ... |
b41c2bc25fd0ed0bbd6568c0a7d9adcfcd4a35edeb00adf80eeafd3c3229ca29 | C | 6,810 | 256 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#include <stdint.h>
#include <stdlib.h>
#include "parasail.h"
#include "memory.h"
#include "sg_helper.h"
#define NEG_INF_32 (INT32_MIN/2)
#define MAX(a,b) ((a)>(b)?(a):(b))
#ifdef PARASA... |
b398fa81e2da54f5200303bd310d74bda0cec575b8d14d3859db33aca2a7b386 | C | 6,843 | 188 | /*
COPYRIGHT
Copyright (C) 2015 Kyle Briggs (kbrig035<at>uottawa.ca)
This section of the code implements an algorithm used in MOSAIC,
which can be found here: http://usnistgov.github.io/mosaic/html/
and takes advantage of a modified version of lmfit-6.1, which
can b... |
dfbfd11936072f5861c19ea2baf9e3f8ccf75c96aa52dafa2725a112899501c1 | C | 6,885 | 202 |
/******************************************************************************
*
* 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://... |
fee154ca6753df5a744ba5881f4cb261ab2ab89d2eb7328ff0ec3863d06fcd4d | C | 6,900 | 285 |
/******************************************************************************
*
* 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:
* ... |
01a60282a4c443ef9f9981adc79c6da9ae35557c85a29ff9bf10ea08c1b70508 | C | 6,915 | 216 | /*--------------------------------------------------------------------------
* voxelizeC.c script is used generate voxelized 3D image matrix from sparse points
*
** Developed and maintained by Kannan Umadevi Venkataraju <[email protected]>
** do not distribute without permission.
*
* Usage
* mexFunction( int nl... |
c1d886491270b2df3c3aa5a455a2f061f4651e8bf23fbe71eb8657024c312584 | C | 6,920 | 96 | #include "build.h"
void CaRU() {
p_O_RyR = Y_ooo[indx] + Y_coo[indx] + Y_cco[indx] + Y_oco[indx];
p_O_RyR_t = ((1))*p_O_RyR + p_O_RyR_base;
J_Ca_rel = ((1.8))*P_RyR * p_O_RyR_t * (Ca_2_SRrl - Ca_2_jnc[indx]) * Sc_Cell;
Ca_2_nd_00 = Ca_2_jnc[indx];
Ca_2_nd_L0[indx] = (Ca_2_nd_00 + f_L * delta_RTF * Vm[indx] * e... |
d9d1a7a8361d2cc8b132585a2d5c2fba15fe36787a0608ea28dcef7aa80b2968 | C | 6,943 | 226 | // Copyright (c) 2008, Casey Duncan (casey dot duncan at gmail dot com)
// Copyright (c) 2022, Max Shinn
// see LICENSE.txt for details
#include "Python.h"
#include <math.h>
#include <stdio.h>
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#ifdef _MSC_VER
#define inline __inline
#end... |
b5581911e61eccf7c343235d7aa20adbb58359de4942ec6666b16f1be5cd1ecf | C | 6,948 | 188 | #include <stdio.h>
#include <climits>
#include "mmpriv.h"
void mm_idxopt_init(mm_idxopt_t *opt)
{
memset(opt, 0, sizeof(mm_idxopt_t));
opt->k = 15, opt->w = 50, opt->flag = 0;
opt->bucket_bits = 14;
opt->mini_batch_size = 50000000;
opt->batch_size = 4000000000ULL;
}
void mm_mapopt_init(mm_mapopt_t *opt)
{
memse... |
3f4a4c70c6887cc34048a5daf75b3d6e3517de878a9d97374da71100b9b64d49 | C | 6,951 | 244 | #include "config.h"
#include <assert.h>
#include <ctype.h>
#include <stddef.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "parasail.h"
#include "memory.h"
#if defined(_MSC_VER)
#define snprintf _snprintf
#endif
/* 0123456789 */
#define BAM_CIGAR_STR "... |
e5960a6882f06afa47bb8fcbe3afc202cc6e573217b3e68e8d87d465e9c5329b | C | 6,984 | 254 | /*
* 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... |
d67a7d342391e0c357606e5eb47bd9d6d983979b56c6c3f641198229b8c0c9b8 | C | 7,004 | 237 | /*
* 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... |
82201b4731b52a822ab497e49473e97089569d3a01e678e87b93d7790186fbb2 | C | 7,017 | 257 | /*
* 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... |
0a80c5fd53be7469c69f2c47ac8ca47acf3917b41f9e81c07884f864c5e7a5c0 | C | 7,019 | 213 | //
// Created by sachetto on 30/09/17.
//
#include "../../3dparty/stb_ds.h"
#include "../../logger/logger.h"
#include "grid.h"
/**
* Decides if the grid should be refined by traversing the whole grid, according
* to parameters refinementLevel and refinementBound. A cell will not be refined
* either if its refineme... |
1665e845aa72c84067a38918ff0b42fc535bc95324fb8aa1767e1fa1ecb4ae33 | C | 7,043 | 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... |
b312c5efe5c9a4edeffbad205633cc869331876a523cce6896f89fc1b2e0b2bb | C | 7,044 | 309 | /*
* steam.c - lmbench version of John McCalpin's STREAM benchmark
*
* usage: stream
*
* 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... |
7632fa6f4e68b6f0397842c8cc5163df4ff8c9649e405c883fb9dc2c748b8080 | C | 7,062 | 152 | #include"build.h"
void dump_real_mpi_IO(double *data, char filename0[100])
{
//printf("it came here, data out \n");
/*for(ii = 1; ii <= mypoints; ii++) {
for(jj = 1; jj <= y_space; jj++) {
for(kk = 1; kk <= z_space; kk++) {
int ind = (ii-1)*y_space*z_space + (jj-1)*z_space + (kk-1);
... |
f22a97183478b562cf337ee7f6c18ddc1f64b8bbce44fd3d688af1a55302b7fa | C | 7,085 | 225 |
/******************************************************************************
*
* 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:
* ... |
cd99137cc0f073219119935b75d9353651668b93acfd2e98e425bd5b17089a83 | C | 7,093 | 294 |
/******************************************************************************
*
* 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:
* ... |
fadebd52c2ba62063e423f088fe1b9f992706aec611a94297d8e42fd9c69d53e | C | 7,112 | 235 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#include <stdint.h>
#include <stdlib.h>
#include "parasail.h"
#include "memory.h"
#define SG_TRACE
#include "sg_helper.h"
#define NEG_INF_32 (INT32_MIN/2)
#define MAX(a,b) ((a)>(b)?(a):(b... |
e98e89ea83b21fe5e5d7bec5e812c1f993eaeba280b43ec961e778b0dc97ea03 | C | 7,184 | 247 |
/******************************************************************************
*
* 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://... |
71a960aed5f55565c690432cfab00fc4e8c45c72b99438a348418c082b347251 | C | 7,247 | 255 | ////
//// Created by sachetto on 06/10/17.
////
#include <criterion/criterion.h>
#include "../alg/grid/grid.h"
#include "../config/linear_system_solver_config.h"
#include "../utils/file_utils.h"
#include "../3dparty/ini_parser/ini.h"
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
real_cpu calc_mse(... |
d693c22f0691172e7e44497e87da1c269d0b5545baabb7366aa9346d7a80d9b6 | C | 7,284 | 244 | #include <ctype.h>
#include <float.h>
#include <stdio.h>
#include <stdlib.h>
#include "3dparty/sds/sds.h"
#include "3dparty/stb_ds.h"
#include "common_types/common_types.h"
#include "config/config_parser.h"
#include "utils/file_utils.h"
struct elem {
struct point_3d n1;
struct point_3d n2;
struct point_3d... |
f303650b564d597999784c13d2925e0e6cb5aa4bfdb8b90cb0bb1a065760169a | C | 7,349 | 231 | //========================================================================
// GLFW 3.4 Wayland - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2014 Jonas Ådahl <[email protected]>
//
// This software is provided 'as-is', without any express or implied
// warrant... |
3be169b894fbdffce2899d0828b4402c926e57177f50a8c0fa77f22f19491069 | C | 7,384 | 213 |
/******************************************************************************
*
* 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:/... |
8529c3bc2cd9abe07e56337248f42fa92d5db74e7dc2db9bcfb63894cc82e127 | C | 7,397 | 287 |
/******************************************************************************
*
* 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:
* ... |
b1c37cb8ed40e8eeca56d4b94572fe0396ea5bb0f02db70269e5ec02ca8630c6 | C | 7,398 | 171 | #include "build.h"
void initial_cond()
{
// Global variables to be updated in euler();
// euler variables initialization
I_Kto_Na = 0;
I_f = 0;
I_gap = 0;
E_f = -69.6;//-69.6;
//if (SWITCH == 0) {
int glob_i;
for (ii = 0;ii <= mypoints+1;ii++){
Vm[ii] = -91.4466885079348;
glob_... |
cc37fedda67b33904cabb505174bcc9dbbebe7b1d6ec62eea898d9d717f83941 | C | 7,429 | 317 | #include "common.h"
#include "bits.h"
#include "binBits.h"
static Bits * ALL_ZERO = NULL;
static Bits * ALL_ONE = ( Bits * ) &"ONE";
struct BinBits* binBitsAlloc( int size, int granularity )
{
struct BinBits * bb;
AllocVar(bb);
bb->size = size;
bb->bin_size = (int) ceil( size / (float) granularity );
... |
20623bcdf5a33c49a1686850387e04aaa12265d54d14013dfcabe9d7e6f00d11 | C | 7,446 | 209 | /*
* SPKTIME2COUNT
* Syntax (MATLAB):
* Y = spktime2count(s, neuronIdx, Tw, Ncount, option)
* Description:
* Convert spike times to non-overlapping spike counts per neuron and time bin.
* - s : 2 x Ns double matrix, columns [ts; id] with time in ms and integer neuron ID.
* - neuronIdx : vector of... |
aabf79c0ff278513d9a3851ec28b1c3ead7e8fdc6bd9714ba8849573a6652e1d | C | 7,504 | 297 | /* seems to be under the GNU Lesser GPL, but this version was
* taken directly from L-BFGS-B code from the 199s so it may
* have been a difference license then. It was re-distributed
* under L-BFGS-B under the 3 clause BSD.
* See http://people.sc.fsu.edu/~jburkardt/f_src/linpack/linpack.html
* */
#include "lbfgsb... |
d85d696460cb4010165a6059e5d5572b13cee573a99bcf1d655ca250798a7ac0 | C | 7,506 | 231 | #include"variables.h"
#include"constants.c"
//#include <stdlib.h>
void I_currents()
{
/* INa: Fast Na+ current (inward) */
I_Na=G_Na*pow(m[i],3)*h[i]*j_1[i]*(V[i]-E_Na);
m_inf=1/pow((1+exp((-56.86-V[i])/9.03)),2);
alpha_m=1/(1+exp((-60-V[i])/5));
beta_m=0.1/(1+exp((V[i]+35)/5)) ... |
53d06990a14ef88a39a5d1cd3292753e6182c2a9916b45ab87aef0e279443d86 | C | 7,512 | 307 | /*
* @file
*
* Object finding code that find peaks by identifying local maxima,
* checking if they have a peak like shape, then computing the
* first moment to determine the peak center.
*
* Hazen 09/13
*
* Compilation (windows):
* gcc -c LMMoment.c
* gcc -shared -o LMMoment.dll LMMoment.o
*
* Compila... |
d9a6eb2f2f47d7bce21e6dc3cac559985d6d5ca446d9cea73868878e5ae97b80 | C | 7,530 | 205 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kalloc.h"
/* In kalloc, a *core* is a large chunk of contiguous memory. Each core is
* associated with a master header, which keeps the size of the current core
* and the pointer to next core. Kalloc allocates small *blocks* of memory from
* the c... |
d7f13eb7e72f63f0703f9258c46d06335e260ba9f1170b7eff46275ffd7eb589 | C | 7,565 | 272 | /*
Sample code showing how to read and write PLY polygon files.
Greg Turk, March 1994
*/
#include <stdio.h>
#include <math.h>
#include <ply.h>
/* user's vertex and face definitions for a polygonal object */
typedef struct Vertex {
float x,y,z; /* the usual 3-space position of a vertex */
} Vertex;
... |
20e90987192797bc3f5209c16a7e2efe5f0a67eecb6d65e981b53ec5ed4f4081 | C | 7,566 | 228 | //
// Created by sachetto on 01/11/18.
//
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#include "data_utils.h"
#define COMPRESED_BLOCK_SIZE 1 << 15
void calculate_blocks_and_compress_data(size_t total_data_size_before_compression,
size_t *tot... |
b9cd461880e6af0ba1245630d9c6d90f013780c607d6bfc7f0825878730bcd43 | C | 7,576 | 292 | /*
* bw_mem64d.c - simple memory write bandwidth benchmark
*
* Usage: bw_mem64 [-P <parallelism>] [-W <warmup>] [-N <repetitions>] [-d <delay>] size what
* what: rd wr fwr frd
*
* Copyright (c) 2026 Huang Ying
*
* Distributed under the FSF GPL with additional restriction that results
* may published onl... |
7853e43b2b19caba2f7504ab35aaa43e84a8ecceb554e3387ec620a055d96247 | C | 7,596 | 265 | /* this file is only included by cigar.c, multiple times */
#define D CONCAT3(int, T, _t)
#define UNUSED(expr) do { (void)(expr); } while (0)
#if defined(STRIPED)
#define NAME parasail_cigar_striped_
#define LOC LOC_STRIPED
#else
#define NAME parasail_cigar_
#define LOC LOC_NOVEC
#endif
#define INC ... |
7aa3c8f4217c5ee5e4fe2fbbaa44bc31b4e136bae77c006ab576fc939ded6853 | C | 7,599 | 234 | /*
* Copyright (c) 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,
* t... |
3a14ee6ad4474323fa902bb1fd6cec29f275548177da24b24a2f5f37c40c1ff9 | C | 7,662 | 208 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "3dparty/sds/sds.h"
#include "3dparty/stb_ds.h"
#include "3dparty/ini_parser/ini.h"
#include "config/config_parser.h"
#include "utils/file_utils.h"
#include "vtk_utils/vtk_unstructured_grid.h"
static void convert_file(const char *input, const char *o... |
af18c0f23e34a6d2267740044c5c0963674d687d15cc00c7501d3cf0b3cfc1af | C | 7,725 | 137 |
/******************************************************************************
*
* 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://... |
ed822b49ebd89424f26eb40f3a460f36822c555846d9e0b882219f240af16e4b | C | 7,732 | 281 |
/******************************************************************************
*
* 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:
* ... |
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