sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2e0b4284620082f63b144da8096b207e9e9590c0e599834332b90624db0cc4a8 | TypeScript | 120,273 | 2,261 | declare module 'node:fs' {
export * from 'fs';
}
declare module 'fs' {
import * as stream from 'node:stream';
import EventEmitter = require('node:events');
import { URL } from 'node:url';
import * as promises from 'node:fs/promises';
export { promises };
/**
* Valid types for path val... |
a106a0bea088b70879ac88ff606dc253c0cc474ea05ad3a282b8bfb1091ae576 | TypeScript | 120,301 | 2,262 | declare module 'node:fs' {
export * from 'fs';
}
declare module 'fs' {
import * as stream from 'node:stream';
import EventEmitter = require('node:events');
import { URL } from 'node:url';
import * as promises from 'node:fs/promises';
export { promises };
/**
* Valid types for path val... |
05fbe81f09fc455a2c343d2458d2b3c600c90b92b22926be765ee79326be9466 | TypeScript | 122,095 | 3,048 | // tslint:disable-next-line:dt-header
// Type definitions for inspector
// These definitions are auto-generated.
// Please see https://github.com/DefinitelyTyped/DefinitelyTyped/pull/19330
// for more information.
// tslint:disable:max-line-length
/**
* The inspector module provides an API for interacting with the ... |
fbdcb7944fbcca2c367e9faf017c4b607f76fa5a1fac6b488c796d18e72120e7 | C | 358 | 13 | #include "parallelReadTiff.h"
#include <time.h>
int main(){
clock_t begin = clock();
void* test = readTiffParallelWrapper("C:\\Users\\Matt\\Desktop\\testTiff\\test.tif");
if(!test) return 1;
clock_t end = clock();
double time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
printf("%f\n",time_sp... |
a680561d0f23c7e6ed621198693720fdcf758706cae1885cc3447abcc7439ccc | C | 683 | 37 | #include <stdarg.h>
#include <stdio.h>
#include "kstring.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
int bwa_kvsprintf(kstring_t *s, const char *fmt, va_list ap)
{
va_list ap2;
int l;
va_copy(ap2, ap);
l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
if (l + 1 > s->m - s->l) {
s->m = s->l ... |
39e717bac1e04027fa2be0d4375b8efc1669fcf80816ba571ddfc97cd59afcb6 | C | 1,449 | 57 | #include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>
#ifdef USE_MALLOC_WRAPPERS
/* Don't wrap ourselves */
# undef USE_MALLOC_WRAPPERS
#endif
#include "malloc_wrap.h"
void *wrap_calloc(size_t nmemb, size_t size,
const char *file, unsigned int line, const char *func) {
void *p = calloc(... |
e7d7722d53795a040d2cfbb1e12f8ee798be6eabaf3bff4068626f4281382a3b | C | 1,650 | 67 | #include <zlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <limits.h>
#include <string.h>
#include <unistd.h>
#include "bwa.h"
#include "bwamem.h"
#include "kseq.h"
KSEQ_DECLARE(gzFile)
int main_maxk(int argc, char *argv[])
{
int i, c, self = 0, max_len = 0;
uint8_t *cnt = 0;
uint64_t hist[256];
bwt_t *bwt;... |
b12fa61858537252504f3444546845438eb4b57ebece228834370483c2695fa2 | C | 1,844 | 60 | #include <stdio.h>
#include <zlib.h>
#include <string.h>
#include <errno.h>
#include <assert.h>
#include "bwamem.h"
#include "kseq.h" // for the FASTA/Q parser
KSEQ_DECLARE(gzFile)
int main(int argc, char *argv[])
{
bwaidx_t *idx;
gzFile fp;
kseq_t *ks;
mem_opt_t *opt;
if (argc < 3) {
fprintf(stderr, "Usage: b... |
1a12bcab36698bfd908f47edf7206359e612abd09b2ef14662ccb2f9eae3d3fb | C | 2,229 | 81 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file stm32f4xx_hal_msp.c
* @brief This file provides code for the MSP Initialization
* and de-Initialization codes.
********************************************... |
b06aa14846c30612c7d7b3783f15cf877c57ec4bba4794c7deb6d137ff490fe7 | C | 2,255 | 75 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file gpio.c
* @brief This file provides code for the configuration
* of all used GPIO pins.
******************************************************************************
*... |
9979269dc2ab997dcd756154cb90db886b8148ccae29c7bae5d45aff3eea93d6 | C | 2,474 | 100 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : usb_device.c
* @version : v1.0_Cube
* @brief : This file implements the USB Device
*************************************************************************... |
2475b60a0664fbc154ae31a3ddb983f27f335979c93153c01939f382ef5c43a2 | C | 2,682 | 98 | #include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "bwt_lite.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
int is_sa(const uint8_t *T, int *SA, int n);
int is_bwt(uint8_t *T, int n);
bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
{
bwtl_t *b;
int i;
b = (bwtl_t*)calloc(1, si... |
513343ad21478f78df1703fb03791467c7fed304e861acb54202de534b220ec6 | C | 3,063 | 112 | #include <stdio.h>
#include "bwtsw2.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
typedef struct {
uint32_t tbeg, tend;
int qbeg, qend;
uint32_t flag:1, idx:31;
int chain; // also reuse as a counter
} hsaip_t;
#define _hsaip_lt(a, b) ((a).qbeg < (b).qbeg)
#include "ksort.h"
KSORT_INIT(hsaip, h... |
8f105b2c05ff004d265b8bf1bf1ae8a4b108010ac3315a67f167df7b4ac8570f | C | 3,744 | 147 | #include <pthread.h>
#include <stdint.h>
#include <stdlib.h>
#include <limits.h>
/************
* kt_for() *
************/
struct kt_for_t;
typedef struct {
struct kt_for_t *t;
long i;
} ktf_worker_t;
typedef struct kt_for_t {
int n_threads;
long n;
ktf_worker_t *w;
void (*func)(void*,long,int);
void *data;... |
352b0f2350cf0b8399a2a1fb88836d376a552faeb880a45729fa08c21a31d5f9 | C | 3,818 | 89 | #include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <math.h>
#include "bwt.h"
#include "bwtsw2.h"
#include "utils.h"
#include "bwa.h"
int bwa_bwtsw2(int argc, char *argv[])
{
bsw2opt_t *opt;
bwaidx_t *idx;
int c;
opt = bsw2_init_opt();
srand48(11);
while ((c = getopt(argc, ar... |
32cdca574b498a6551e48063fdc12d8a60335c60b8343161d2ea093cfb0f2e16 | C | 3,887 | 126 | #include "tiffio.h"
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include "mex.h"
//mex -v COPTIMFLAGS="-O3 -fwrapv -DNDEBUG" CFLAGS='$CFLAGS -O3 -fopenmp' LDFLAGS='$LDFLAGS -O3 -fopenmp' '-I/global/home/groups/software/sl-7.x86_64/modules/libtiff/4.1.0/libtiff/' '-L/global/home/groups/software/sl-7.x86_6... |
602a4a0ccaf477b7c44008e60ac9d451d823af18c56ddbfdcdd7f7b8c12cfebc | C | 4,318 | 171 | #include <string.h>
#include "event.h"
#include "neural_manifold.h"
extern bool run_flag;
extern Matrix* input_data;
/**
*@function ¼ÆËãУÑéÂë
*@param Event *packet ʼþÊý¾Ý°ü
*@return ErrorStatus Ö´ÐÐ״̬
*/
static unsigned char calcCheckCode(Event *packet)
{
if(NULL == packet)return false;
... |
4584eda1447326efc187b4d51a43fa474baf1b0c1a742fdbff43763a26c29cdc | C | 4,821 | 191 | #include <string.h>
#include <assert.h>
#include <stdlib.h>
#include <stdio.h>
#include "rle.h"
const uint8_t rle_auxtab[8] = { 0x01, 0x11, 0x21, 0x31, 0x03, 0x13, 0x07, 0x17 };
// insert symbol $a after $x symbols in $str; marginal counts added to $cnt; returns the size increase
int rle_insert_cached(uint8_t *block,... |
047c63014d1242a8d4254495d019f710bead71de566897c6daaf97f496a019b4 | C | 5,017 | 224 | /**
******************************************************************************
* @file usbd_ioreq.c
* @author MCD Application Team
* @brief This file provides the IO requests APIs for control endpoints.
******************************************************************************
* @attenti... |
fa6a943e3e1e2b544f5a0c1cef3c4197d213abfcb7b2bc09c4eb3f56f9a687ff | C | 5,764 | 217 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file stm32f4xx_it.c
* @brief Interrupt Service Routines.
******************************************************************************
* @attention
*
* Copyright (c) 2025 STMicr... |
8155c9528341d9b86834e750004f9ddc3d1b84def82cd85848663acc66d4f704 | C | 5,810 | 172 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
59d52234e9ec80f51b3c0ce98a06aca773f2673ae45ccc0d0f7d87527e15a288 | C | 5,865 | 217 | #include <sys/types.h>
#include <sys/mman.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <unistd.h>
#include <fcntl.h>
#include <errno.h>
#include <stdio.h>
#include "bwa.h"
#ifndef PATH_MAX
# define PATH_MAX 1024
#endif
int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
... |
7724413fe25e325e466a6f891a0c9a1a96311b23dea85f8cb6441143a5a73412 | C | 5,865 | 130 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
edbac14312186e3b128567e6c7f47880d5c1cc5d371e3bfc89ccd2ddc5f891b6 | C | 6,034 | 247 | /**
******************************************************************************
* @file usbd_cdc_if_template.c
* @author MCD Application Team
* @brief Generic media access Layer.
******************************************************************************
* @attention
*
* Copyright (c... |
02cdfabe6d3e7cd00ccb0f2d40e1ec7f05a2a9e51f090451caa3e11ce089bb16 | C | 6,098 | 210 | #include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <stdio.h>
#include <errno.h>
#include "bamlite.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
/*********************
* from bam_endian.c *
*********************/
static inline int bam_is_big_endian()
{
long one= 1;
return !(*((c... |
1846c52158a88520b248b280436bd8bbf5e42b810e1c04ca4205e14ffea23d17 | C | 6,470 | 248 | /*<html><pre> -<a href="index_r.htm#TOC"
>-------------------------------</a><a name="TOP">-</a>
random_r.c and utilities
Park & Miller's minimimal standard random number generator
argc/argv conversion
Used by rbox. Do not use 'qh'
*/
#include "libqhull_r.h"
#includ... |
800d76fcc344a3f36c22bf8893f071fb6526fe951b2f5700e3f4512cdfe6db2e | C | 6,674 | 223 | /*
* sais.c for sais-lite
* Copyright (c) 2008 Yuta Mori All Rights Reserved.
*
* 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 ... |
239182eecd997f1cc9b15bc7b3815e3ea9d10a39cda0ca5f318967f4b42901eb | C | 6,864 | 235 | #include <zlib.h>
#include <ctype.h>
#include "bwtaln.h"
#include "utils.h"
#include "bamlite.h"
#include "kseq.h"
KSEQ_DECLARE(gzFile)
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
extern unsigned char nst_nt4_table[256];
static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, ... |
7d06a4071bb3882329676fccba3eb0095aad31615bab24a91c8cd5a5974417f4 | C | 6,921 | 248 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : main.c
* @brief : Main program body
******************************************************************************
* @attention
*
* Copyright (c) 2025 STMicr... |
e6172e353f51a8899d1edfe752597e57ac7fd8248a1c4c7f7f83d6deef6c7961 | C | 7,169 | 306 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
fe74e77c09d965bd692db6434eb3b1bc00fac01a4967245aa6bb874c44d52627 | C | 7,179 | 282 | /**
******************************************************************************
* @file usbd_conf_template.c
* @author MCD Application Team
* @brief USB Device configuration and interface file
* This template should be copied to the user folder,
* renamed and customized foll... |
2332154ea25210d9f5447fb3ab3acc7409a614628108c3efbe8d818acadb12da | C | 8,825 | 291 | #include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <zlib.h>
#include <pthread.h>
#include <errno.h>
#include "ksw.h"
#include "kseq.h"
#include "kstring.h"
#include "bwa.h"
#include "utils.h"
KSEQ_DECLARE(gzFile)
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
#define... |
a2b61dfbc4e9472dbf8caf15182bf75e5ef49ecee58e53574accd0ee923115a2 | C | 9,019 | 318 | #include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdio.h>
#include <zlib.h>
#include "rle.h"
#include "rope.h"
/*******************
*** Memory Pool ***
*******************/
#define MP_CHUNK_SIZE 0x100000 // 1MB per chunk
typedef struct { // memory pool for fast and compact memory allocation (n... |
c55986d1ffcc42e8cb4311dcba1b93c71d03a3ffcfa421297c26df44e43d35bb | C | 9,155 | 264 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "bwtgap.h"
#include "bwtaln.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
#define STATE_M 0
#define STATE_I 1
#define STATE_D 2
#define aln_score(m,o,e,p) ((m)*(p)->s_mm + (o)*(p)->s_gapo + (e)*(p)->s_gape)
gap_stack_t *gap_init_s... |
02f567a178484e277646fbdbafb0a2ca6e7d0066d5f062e5fcdc420822cd1829 | C | 9,520 | 338 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : usbd_cdc_if.c
* @version : v1.0_Cube
* @brief : Usb device for Virtual Com Port.
***************************************************************************... |
f14d5887f2b0717655a1d9a4944dbc0417d504564bcf3fa639fa349fe3eef8fd | C | 9,714 | 374 | #include <stdio.h>
#include <fcntl.h>
#include <errno.h>
#include <ctype.h>
#include <unistd.h>
#include <string.h>
#include <stdlib.h>
#include <signal.h>
#include <sys/wait.h>
#include <sys/types.h>
#ifndef _WIN32
#include <netdb.h>
#include <arpa/inet.h>
#include <sys/socket.h>
#endif
#ifdef USE_MALLOC_WRAPPERS
# ... |
6fe9435206369f413891bbd6d2fec28a56a4c71777e49c609c057fa4ca706c43 | C | 9,900 | 323 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
411744c3b993bd067df0f7276a7fa0ffa1276f505e20f0c474fd56bd2695aee8 | C | 9,989 | 326 | #include <math.h>
#include <stdint.h>
#include <stdlib.h>
#include <stdbool.h>
#include <stdio.h>
#include <assert.h>
#include "tiffio.h"
#include "lzwEncode.h"
#define SIZEOF_WORDTYPE SIZEOF_SIZE_T
typedef size_t WordType;
/*
* NB: The 5.0 spec describes a different algorithm than Aldus
* implements. Specifica... |
185c5489c2f5721ae7c26f334839e493951f83c827757dd9d793aef86a38c312 | C | 10,517 | 274 | #include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "utils.h"
#include "bwt.h"
#include "bntseq.h"
#include "bwtsw2.h"
#include "kstring.h"
#include "ksw.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
#define MIN_RATIO 0.8
#define OUTLIER_BOUND 2.0
#define MAX_ST... |
3176e6961a4ad2b89a9cc715203b6fd87ed5fbbda6c4f57c1d390412ff755225 | C | 11,017 | 321 | #include <stdio.h>
#include <unistd.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <stdint.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "bwtaln.h"
#include "bwtgap.h"
#include "utils.h"
#include "bwa.h"
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#ifdef USE_... |
a97ae988ac3c42c19031fd0b0d8e0a883604f888604db6ce0feded025d511995 | C | 11,899 | 326 | #include <stdlib.h>
#include <math.h>
#include "parallelReadTiff.h"
//mex -v COPTIMFLAGS="-O3 -fwrapv -DNDEBUG" CFLAGS='$CFLAGS -O3 -fopenmp' LDFLAGS='$LDFLAGS -O3 -fopenmp' '-I/global/home/groups/software/sl-7.x86_64/modules/libtiff/4.1.0/libtiff/' '-L/global/home/groups/software/sl-7.x86_64/modules/libtiff/4.1.0/libt... |
0d62ac7c438646f1c75b54beb6ceac2ef7a768fd4de19218630cfa1fd1296a46 | C | 12,165 | 445 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : App/usbd_desc.c
* @version : v1.0_Cube
* @brief : This file implements the USB device descriptors.
*********************************************************... |
6105fe093fdccb58accb2e2e6b60aa7f0b5c6fd3c657e4facc5bd7df92e17bbf | C | 12,638 | 402 | /* QSufSort.c
Original source from qsufsort.c
Copyright 1999, N. Jesper Larsson, all rights reserved.
This file contains an implementation of the algorithm presented in "Faster
Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
Sadakane (sada@is.s.u-tokyo.ac.jp).
This software ma... |
46c48db288088f17d660247ed1e258ca173dac430b63d10c84458cd6feb1c1b1 | C | 13,988 | 451 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
7ace4af22ac910599faa51ba795efd606c3ce6d7a7c1526fc376fc9d57d1ecb1 | C | 15,342 | 469 | /* The MIT License
Copyright (c) 2008 Genome Research Ltd (GRL).
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... |
f86259bdd2ab4b32036e288e5c69cf20d443ccdb2af644c7fa1bc880207563a5 | C | 15,756 | 502 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
0089963a5a1958b702279bd030ce44d50482be9d81b118ce9d6488133c45beb0 | C | 17,758 | 452 | /**
******************************************************************************
* @file usbd_desc_template.c
* @author MCD Application Team
* @brief This file provides the USBD descriptors and string formatting method.
* This template should be copied to the user folder,
* r... |
827a13ab9d93f62235073485a9781982b5f2786d573b77dae5f052e71a2c87f6 | C | 18,618 | 419 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
b40c59290e0a01e78b016c85c71cc8e28e630bdff897bf986d70ecc2e13a629c | C | 18,944 | 500 | #include <stdint.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include "lzwEncode.h"
#include "tiffio.h"
#include "omp.h"
#include "mex.h"
//mex -v COPTIMFLAGS="-O3 -DNDEBUG" CFLAGS='$CFLAGS -O3 -fopenmp' LDFLAGS='$LDFLAGS -O3 -fopenmp' '-I/global/home/groups/software/sl-7.x86_64/m... |
14f0ee9302daac1ee27e4b9f02e1be1c2e8effa130ef2ccae30ab6d9d6edd7d0 | C | 18,955 | 619 | #include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <sys/resource.h>
#include <assert.h>
#include "bwt_lite.h"
#include "bwtsw2.h"
#include "bwt.h"
#include "kvec.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
typedef struct {
bwtint_t k, l;
} qintv_t;
#define qintv_eq(a, b) ((a).k ... |
e30358af4eb97f5925035417de461cd5e47c2cc2761ee24e77101a9c50e297f3 | C | 19,482 | 671 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file : Target/usbd_conf.c
* @version : v1.0_Cube
* @brief : This file implements the board support package for the USB device library
*****************************... |
c1c89d6d3908e5aee22bdf3883dc74f1b5b520d57637081a842e060ac82df5db | C | 19,566 | 606 | #include <unistd.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <assert.h>
#include "bwase.h"
#include "bwtaln.h"
#include "bntseq.h"
#include "utils.h"
#include "kstring.h"
#include "bwa.h"
#include "ksw.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.... |
e213dcdd1b15178a434020f46c334a53eaaabedb0bf4a6989a3b8ad264ba2b4b | C | 20,848 | 535 | /*<html><pre> -<a href="qh-user_r.htm"
>-------------------------------</a><a name="TOP">-</a>
user.c
user redefinable functions
see user2_r.c for qh_fprintf, qh_malloc, qh_free
see README.txt see COPYING.txt for copyright information.
see libqhull_r.h for data structu... |
5e1aaefe546fbf8cc1f964e9e00558971e197a01a3ec451be3c8058f73eca667 | C | 21,027 | 483 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
104de04ff5f3664f8cfad66e2caa1718895ac058e72302f79c979d4a1ede3cdb | C | 21,438 | 562 | /*<html><pre> -<a href="qh-mem_r.htm"
>-------------------------------</a><a name="TOP">-</a>
mem_r.c
memory management routines for qhull
See libqhull/mem_r.c for a standalone program.
To initialize memory:
qh_meminit(qh, stderr);
qh_meminitbuffers(qh, qh->IStracing... |
94796f7a106174496931af4297bfe59c8b8b1ae3c72d1f0b2c7ea3dc67a17a99 | C | 24,964 | 776 | #include <stdlib.h>
#include <stdio.h>
#include <math.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#include "bntseq.h"
#include "bwt_lite.h"
#include "utils.h"
#include "bwtsw2.h"
#include "kstring.h"
#include "bwa.h"
#include "ksw.h"
#include "kseq.h"
KSEQ_DECLARE... |
b3cec933f5b27094d06407ccf45f94aca8f966506c50f07c3ee426942eb2f608 | C | 25,609 | 842 | /*<html><pre> -<a href="index_r.htm#TOC"
>-------------------------------</a><a name="TOP">-</a>
rboxlib_r.c
Generate input points
notes:
For documentation, see prompt[] of rbox_r.c
50 points generated for 'rbox D4'
WARNING:
incorrect range if qh_RANDOMmax ... |
08302a5e0379cd85428ae2a17d3d43420c9c47d8233f91a8813a0bddfc087b1d | C | 25,675 | 1,051 | /**
******************************************************************************
* @file usbd_req.c
* @author MCD Application Team
* @brief This file provides the standard USB requests following chapter 9.
******************************************************************************
* @attent... |
e2dcbb8ffb5a8c1fb11e0ab3e3994f5ccbc163abf32041028f3ea6b3c4c42805 | C | 27,175 | 749 | /* The MIT License
Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation t... |
cdec0a2a4f0cfde6eae5bc16fce9466367fb3e2986bdfaa673822b64548958fe | C | 27,589 | 747 | /**
******************************************************************************
* @file system_stm32f4xx.c
* @author MCD Application Team
* @brief CMSIS Cortex-M4 Device Peripheral Access Layer System Source File.
*
* This file provides two functions and one global variable to be called fro... |
eabd8493f0f71436d9885a7e928f6ec03855a117576134e35d65342611bbf2b8 | C | 28,306 | 875 | /**
******************************************************************************
* @file usbd_cdc.c
* @author MCD Application Team
* @brief This file provides the high layer firmware functions to manage the
* following functionalities of the USB CDC Class:
* - Initialization... |
2862511b3afcdb92cd21cc0205a9aefbf746119a58bcb4ee06a78ed1d1161840 | C | 29,396 | 784 | #include <unistd.h>
#include <math.h>
#include <stdlib.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include "bwtaln.h"
#include "kvec.h"
#include "bntseq.h"
#include "utils.h"
#include "bwase.h"
#include "bwa.h"
#include "ksw.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
typedef stru... |
7ecfe9054c7c94fee92fab0986a682948750ee7c226f5cd17333fe33518565fd | C | 30,107 | 762 | #include <stdio.h>
#include <stdint.h>
#include <math.h>
#include <string.h>
#include <unistd.h>
#include <fcntl.h>
#include <limits.h>
#include "tiffio.h"
#include "omp.h"
#include "mex.h"
//mex -v COPTIMFLAGS="-O3 -DNDEBUG" CFLAGS='$CFLAGS -O3 -fopenmp' LDFLAGS='$LDFLAGS -O3 -fopenmp' '-I/global/home/groups/software... |
e66d8781093fe67b68277a4b0768aa749aac31e186cfe804324b104eb5bdf276 | C | 30,324 | 683 | /*<html><pre> -<a href="qh-stat_r.htm"
>-------------------------------</a><a name="TOP">-</a>
stat_r.c
contains all statistics that are collected for qhull
see qh-stat_r.htm and stat_r.h
Copyright (c) 1993-2018 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull_r/... |
61b0edbeb0e9c921dd8580eeeb18c85f0ddd1fa0a6228b592076667148acae78 | C | 30,614 | 1,220 | /**
******************************************************************************
* @file usbd_core.c
* @author MCD Application Team
* @brief This file provides all the USBD core functions.
******************************************************************************
* @attention
*
* Cop... |
96f5a2a2f62252722b03e707e77dcfc45490be0323238b0117d3ee23e082e3b3 | C | 34,690 | 1,340 | /*<html><pre> -<a href="qh-set_r.htm"
>-------------------------------</a><a name="TOP">-</a>
qset_r.c
implements set manipulations needed for quickhull
see qh-set_r.htm and qset_r.h
Be careful of strict aliasing (two pointers of different types
that reference the same l... |
397d6396527433916503bf622ab3c6055dbc6a28aae632e6a2c867d17bfea3f1 | C | 45,785 | 1,273 | /*<html><pre> -<a href="qh-geom_r.htm"
>-------------------------------</a><a name="TOP">-</a>
geom_r.c
geometric routines of qhull
see qh-geom_r.htm and geom_r.h
Copyright (c) 1993-2018 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull_r/geom_r.c#14 $$Change: 254... |
bf40dac45d1855a591e43d453cbe7abf5c99e0d0e00f83340de9072e165ac59a | C | 47,472 | 1,317 | /*<html><pre> -<a href="qh-poly_r.htm"
>-------------------------------</a><a name="TOP">-</a>
poly_r.c
implements polygons and simplices
see qh-poly_r.htm, poly_r.h and libqhull_r.h
infrequent code is in poly2_r.c
(all but top 50 and their callers 12/3/95)
Copyright... |
ea2efc9893b5dbb704509c02d422ea0c6e6525a53bda98f019dd67db4f3100b8 | C | 49,229 | 1,264 | /* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... |
6d7db475d63f5935ffc05086d9ebbb8c9207d52ff7322277ba07a28bc0fa832f | C | 53,813 | 1,623 | /*
BWTConstruct.c BWT-Index Construction
This module constructs BWT and auxiliary data structures.
Copyright (C) 2004, Wong Chi Kwong.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Founda... |
dd2c0a8c8e6137b67ca8aac6748172585c35c9eea32b3955b23b17db2951485d | C | 66,346 | 1,654 | /*<html><pre> -<a href="qh-qhull_r.htm"
>-------------------------------</a><a name="TOP">-</a>
libqhull_r.c
Quickhull algorithm for convex hulls
qhull() and top-level routines
see qh-qhull_r.htm, libqhull.h, unix_r.c
see qhull_ra.h for internal functions
Copyright ... |
66f43d43313bc2eedce2773864265efcb61ecb3eb70fab9e8a7839df6eee435a | C | 73,854 | 2,268 | /*<html><pre> -<a href="qh-geom_r.htm"
>-------------------------------</a><a name="TOP">-</a>
geom2_r.c
infrequently used geometric routines of qhull
see qh-geom_r.htm and geom_r.h
Copyright (c) 1993-2018 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull_r/geom2... |
f902776f52438d7dfb5450ba22e699f67c9a41891503dd28169d55dba13fd41b | C | 75,784 | 2,129 |
/*<html><pre> -<a href="qh-globa_r.htm"
>-------------------------------</a><a name="TOP">-</a>
global_r.c
initializes all the globals of the qhull application
see README
see libqhull_r.h for qh.globals and function prototypes
see qhull_ra.h for internal functions
... |
9da4b8675c640432f7a4c04b4bfb86745dde97cb33645e9386cf1b97cd8e9b6c | C | 140,430 | 4,115 | /*<html><pre> -<a href="qh-io_r.htm"
>-------------------------------</a><a name="TOP">-</a>
io_r.c
Input/Output routines of qhull application
see qh-io_r.htm and io_r.h
see user_r.c for qh_errprint and qh_printfacetlist
unix_r.c calls qh_readpoints and qh_produce_outpu... |
394551afba8fc6893e3cf4a4de0f9a4e3bee4788fcb9d8962dccbf586dd964af | C | 145,471 | 3,699 | /*<html><pre> -<a href="qh-poly_r.htm"
>-------------------------------</a><a name="TOP">-</a>
poly2_r.c
implements polygons and simplicies
see qh-poly_r.htm, poly_r.h and libqhull_r.h
frequently used code is in poly_r.c
Copyright (c) 1993-2018 The Geometry Center.
$... |
0bcbf0dfdbe917cc97f5b0f03eac971211c396a10c0efe35e66b9c928a795ddf | C | 200,000 | 5,165 | /*<html><pre> -<a href="qh-merge_r.htm#TOC"
>-------------------------------</a><a name="TOP">-</a>
merge_r.c
merges non-convex facets
see qh-merge_r.htm and merge_r.h
other modules call qh_premerge() and qh_postmerge()
the user may call qh_postmerge() to perform additi... |
4dff04101bd64b95c8f708d1accd1bedc39e95a263444290f796c63f4734d4cd | C++ | 25 | 1 | #include "precompiled.h"
|
e18563a4652068dee9a43d1d6bdddc07b581f9d54856a58042f0597a5cf538a3 | C++ | 39 | 2 | #include "precompiled.h"
int main() {}
|
194b3879bc6733ef43b13625fe522778afd2df2e5e72c68bb2a85e575bff52db | C++ | 64 | 6 | #include "configparam.h"
ConfigParam::ConfigParam()
{
}
|
9cae989a7ff37ed7d1c6ac0b9e13fabc53857e7f82c6e6d3dc58d358479f5699 | C++ | 204 | 6 | #define NS_PRIVATE_IMPLEMENTATION
#define CA_PRIVATE_IMPLEMENTATION
#define MTL_PRIVATE_IMPLEMENTATION
#include <Foundation/Foundation.hpp>
#include <Metal/Metal.hpp>
#include <QuartzCore/QuartzCore.hpp>
|
1f8c2bb02705802a608f063c6755b6aebb1d712ef8f2ddea17d4efd784a7fc75 | C++ | 207 | 10 |
int orderint = (int) order;
for(int jj = 0; jj < x_length; jj++)
{
for(int ii = firstknot[jj]; ii < lastknot[jj]; ii++)
{
Sx[jj + (ii-1)*x_m] = bin(&(knots[-1]),ii,orderint,x[jj]);
}
}
|
94f395ee06e0c2bd1b91f4d2394a7e75d0832f9271b23d2b35b025e4c9b1494a | C++ | 222 | 11 |
int orderint = (int) order;
for(int jj = 0; jj < x_length; jj++)
{
double y0 = y[jj];
for(int ii = firstknot[jj]; ii < lastknot[jj]; ii++)
{
d[ii-1] += y0*bin(&(knots[-1]),ii,orderint,x[jj]);
}
}
|
b553d5867f64e4f1ed70b79cb1a9b12c42307a632b7ab78694e07b796eedc6e1 | C++ | 247 | 13 |
int orderint = (int) order;
for(int jj = 0; jj < x_length; jj++)
{
double s = 0;
for(int ii = firstknot[jj]; ii < lastknot[jj]; ii++)
{
s += weights[ii-1]*bin(&(knots[-1]),ii,orderint,x[jj]);
}
Sx[jj] = s;
}
|
13a7c59bee2cf01f134cbf49095e5077820d04f34c8fe93f71557b331dfa8f74 | C++ | 355 | 10 | #include "basecall/ModelRunnerBase.h"
#include "config/BasecallModelConfig.h"
namespace dorado::basecall {
std::pair<int, int> ModelRunnerBase::batch_timeouts_ms() const {
return config::is_duplex_model(config()) ? std::make_pair(5000, 5000)
: std::make_pair(100, 100);... |
11a1362a638d7830c15ee114a648dc995e1ea64447ce784aa923db7c7fc866fd | C++ | 378 | 15 | #include "utils/concurrency/AsyncExecutor.h"
namespace dorado::utils::concurrency {
void AsyncExecutor::flush() {
assert(m_tasks != nullptr);
m_tasks->wait_for_queue_to_complete(m_q_idx);
}
std::size_t AsyncExecutor::tasks_in_flight() const {
assert(m_tasks != nullptr);
return m_tasks->tasks_in_fligh... |
49c83d4e5bd10e65cf21eae6e6eedd09be46d58d613b99fa049091899d1bf8af | C++ | 400 | 12 | #include "secondary/features/decoder_factory.h"
#include "secondary/architectures/model_config.h"
namespace dorado::secondary {
std::unique_ptr<DecoderBase> decoder_factory(const ModelConfig& config) {
const LabelSchemeType label_scheme_type = parse_label_scheme_type(config.label_scheme_type);
return std::ma... |
c3a37fbadb2fd050b5135b3f84be2dcc0d9f522a9e585dc1b9f8ea3dba4422eb | C++ | 400 | 25 | #include "hardwarethread.h"
#include "main_widget.h"
#include <QApplication>
#include <QDebug>
#include <QLibrary>
#include <QMessageBox>
#include <QThread>
#include <serial.h>
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
qRegisterMetaType<QList<int>>("QList<int>");
M... |
5c98255bf9942f41f80811455c04a314e244cc925aca5b0bf5886f1e89fcec66 | C++ | 472 | 19 | #include "nn/RMSNorm.h"
#include <c10/core/TensorOptions.h>
#include <spdlog/spdlog.h>
namespace dorado::nn {
RMSNormImpl::RMSNormImpl(int hidden_size_) : hidden_size(hidden_size_) {
weight = at::ones({hidden_size});
register_parameter("weight", weight, false);
}
at::Tensor RMSNormImpl::forward(at::Tensor x... |
22bea2637e1681450a9976505c566efa27dda1227c73320ef46efa1d52ab80d4 | C++ | 568 | 24 | #include "utils/sys_utils.h"
#include <fstream>
#include <string>
namespace dorado::utils {
bool running_in_docker() {
#if defined(__linux__)
// Look for docker paths in the init process.
std::ifstream cgroup_file("/proc/1/cgroup", std::ios_base::in | std::ios_base::binary);
if (cgroup_file.is_open()) {
... |
db96658266002b9e73c4ef9b1b1b6413ee06c4d6a917bae0168b49a8eaeb0cfa | C++ | 571 | 25 | #include "nn/KoiThreads.h"
#include "koi_thread_pool.h"
#include <spdlog/spdlog.h>
#include <stdexcept>
namespace dorado::nn {
KoiThreads::KoiThreads(int num_threads) {
const int ret = koi_create_thread_pool(&m_thread_pool, num_threads);
if (ret != KOI_SUCCESS) {
throw std::runtime_error("Failed to... |
f6db089498dda7b5870d9c0a4a5bd9c4421b7d599f08d640f5d60da00e1f5f67 | C++ | 612 | 27 | #include "utils/basecaller_utils.h"
#include <fstream>
#include <optional>
namespace dorado::utils {
std::optional<std::unordered_set<std::string>> load_read_list(const std::string& read_list) {
std::unordered_set<std::string> read_ids;
if (read_list == "") {
return {};
}
std::ifstream dataF... |
db1f34fb008be58ab5070ea01de1c7074a5e35b127a815beccdc07a855504987 | C++ | 633 | 24 | #include "read_pipeline/nodes/NullNode.h"
namespace dorado {
void NullNode::input_thread_fn() {
Message message;
while (get_input_message(message)) {
// Do nothing with the popped message.
}
}
NullNode::NullNode() : MessageSink(1000, 4) {}
NullNode::~NullNode() { stop_input_processing(utils::Asy... |
fb568ca3bedbd7af22a36dbcb6969f053208f6997e2c8e3918d6c878025ecad9 | C++ | 647 | 23 | #include "utils/io_utils.h"
#include <fstream>
#include <iostream>
#include <ostream>
#include <stdexcept>
namespace dorado::utils {
std::unique_ptr<std::ostream, void (*)(std::ostream*)> get_output_stream(
const std::filesystem::path& out_fn) {
if (std::empty(out_fn)) {
return {&std::cout, [](st... |
a361a2e2461c6dc23e81706e2e514233699030e5f56e143a8afda4eeba51519f | C++ | 672 | 24 | #include "utils/crypto_utils.h"
#if defined(__APPLE__)
#include <CommonCrypto/CommonDigest.h>
#else
#include <openssl/sha.h>
#endif
namespace dorado::utils::crypto {
SHA256Digest sha256(std::string_view data) {
// Digest the data.
SHA256Digest hash{};
#if defined(__APPLE__)
static_assert(std::size(SHA256... |
a99f2e13d5befb4b0a10082dd310d4abea576f4f5b80fe26ad72bfc5e9772835 | C++ | 688 | 22 | #include "hts_types.h"
#include <htslib/faidx.h>
#include <htslib/sam.h>
#include <stdexcept>
namespace kadayashi {
void FaidxDestructor::operator()(faidx_t* faidx) const noexcept { fai_destroy(faidx); }
void HtsIdxDestructor::operator()(hts_idx_t* bam) const noexcept { hts_idx_destroy(bam); }
void SamHdrDestruct... |
63e9f90b864a1b381076f432364dc9229a52fcfc598330273b6515452ab6900d | C++ | 694 | 25 | #include "demux/AdapterDetectorSelector.h"
#include "demux/AdapterDetector.h"
#include "demux/adapter_info.h"
#include <spdlog/spdlog.h>
#include <cassert>
namespace dorado::demux {
std::shared_ptr<AdapterDetector> AdapterDetectorSelector::get_detector(
const AdapterInfo& adapter_info) {
std::string ke... |
577ab5fea3b5b58c650d767e0a208794d0cd941dd50cdec7d4048f7caa97d0f3 | C++ | 722 | 26 | #include "demux/BarcodeClassifierSelector.h"
#include "demux/BarcodeClassifier.h"
#include "demux/barcoding_info.h"
#include <spdlog/spdlog.h>
#include <cassert>
namespace dorado::demux {
std::shared_ptr<const BarcodeClassifier> BarcodeClassifierSelector::get_barcoder(
const BarcodingInfo& barcode_kit_info... |
a863639ded16c392076b8feb0cf730ce021f2326fb35f3941a6542c8faea7e3c | C++ | 780 | 25 | #include "nn/LinearUpsample.h"
#include "config/common.h"
namespace dorado::nn {
LinearUpsampleImpl::LinearUpsampleImpl(const int size, const int scale_factor_)
: scale_factor(scale_factor_) {
linear = register_module(
"linear",
torch::nn::Linear(torch::nn::LinearOptions(size, sca... |
9d9f389aadcad5c050950d86379937b7fe7b9415601109114de79bdf7355f633 | C++ | 783 | 31 | #include "Decoder.h"
#include "config/BasecallModelConfig.h"
#if DORADO_CUDA_BUILD
#include "CUDADecoder.h"
#endif
#include "CPUDecoder.h"
#include <c10/core/Device.h>
namespace dorado::basecall::decode {
std::unique_ptr<Decoder> create_decoder(c10::Device device,
const con... |
b8b02ed3d29f31e2bc102135da35151dcd5c2840d46097be88bff9b1cfaf6794 | C++ | 790 | 31 | #include "alignment/BedFileAccess.h"
#include <cassert>
namespace dorado::alignment {
bool BedFileAccess::load_bedfile(const std::string& bedfile) {
std::lock_guard guard(m_mutex);
auto bed = std::make_shared<BedFile>();
if (!bed->load(bedfile)) {
return false;
}
m_bedfile_lut.emplace(bed... |
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