Mercurial > repos > ashvark > qiime_1_8_0
diff bwa-0.6.2/utils.c @ 0:dd1186b11b3b draft
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:14 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-0.6.2/utils.c Fri Jul 18 07:55:14 2014 -0400 @@ -0,0 +1,164 @@ +/* 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, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* Contact: Heng Li <lh3@sanger.ac.uk> */ + +#include <stdio.h> +#include <stdarg.h> +#include <stdlib.h> +#include <string.h> +#include <zlib.h> +#include <errno.h> +#include <sys/resource.h> +#include <sys/time.h> +#include "utils.h" + +FILE *err_xopen_core(const char *func, const char *fn, const char *mode) +{ + FILE *fp = 0; + if (strcmp(fn, "-") == 0) + return (strstr(mode, "r"))? stdin : stdout; + if ((fp = fopen(fn, mode)) == 0) { + fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn); + abort(); + } + return fp; +} +FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp) +{ + if (freopen(fn, mode, fp) == 0) { + fprintf(stderr, "[%s] fail to open file '%s': ", func, fn); + perror(NULL); + fprintf(stderr, "Abort!\n"); + abort(); + } + return fp; +} +gzFile err_xzopen_core(const char *func, const char *fn, const char *mode) +{ + gzFile fp; + if (strcmp(fn, "-") == 0) + return gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode); + if ((fp = gzopen(fn, mode)) == 0) { + fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn); + abort(); + } + return fp; +} +void err_fatal(const char *header, const char *fmt, ...) +{ + va_list args; + va_start(args, fmt); + fprintf(stderr, "[%s] ", header); + vfprintf(stderr, fmt, args); + fprintf(stderr, " Abort!\n"); + va_end(args); + abort(); +} + +void err_fatal_simple_core(const char *func, const char *msg) +{ + fprintf(stderr, "[%s] %s Abort!\n", func, msg); + abort(); +} + +size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream) +{ + size_t ret = fwrite(ptr, size, nmemb, stream); + if (ret != nmemb) + { + err_fatal_simple_core("fwrite", strerror(errno)); + } + return ret; +} + +int err_printf(const char *format, ...) +{ + va_list arg; + int done; + + va_start(arg, format); + done = vfprintf(stdout, format, arg); + int saveErrno = errno; + va_end(arg); + + if (done < 0) + { + err_fatal_simple_core("vfprintf(stdout)", strerror(saveErrno)); + } + return done; +} + +int err_fprintf(FILE *stream, const char *format, ...) +{ + va_list arg; + int done; + + va_start(arg, format); + done = vfprintf(stream, format, arg); + int saveErrno = errno; + va_end(arg); + + if (done < 0) + { + err_fatal_simple_core("vfprintf", strerror(saveErrno)); + } + return done; +} + +int err_fflush(FILE *stream) +{ + int ret = fflush(stream); + if (ret != 0) + { + err_fatal_simple_core("fflush", strerror(errno)); + } + return ret; +} + +int err_fclose(FILE *stream) +{ + int ret = fclose(stream); + if (ret != 0) + { + err_fatal_simple_core("fclose", strerror(errno)); + } + return ret; +} + +double cputime() +{ + struct rusage r; + getrusage(RUSAGE_SELF, &r); + return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec); +} + +double realtime() +{ + struct timeval tp; + struct timezone tzp; + gettimeofday(&tp, &tzp); + return tp.tv_sec + tp.tv_usec * 1e-6; +}