https://github.com/lh3/bwa
Tip revision: 139f68fc4c3747813783a488aef2adc86626b01b authored by Heng Li on 22 September 2022, 23:52:12 UTC
Merge pull request #367 from martin-g/github-actions-linux-aarch64
Merge pull request #367 from martin-g/github-actions-linux-aarch64
Tip revision: 139f68f
utils.c
/* 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
"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.
*/
#define FSYNC_ON_FLUSH
#include <stdio.h>
#include <stdarg.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <errno.h>
#ifdef FSYNC_ON_FLUSH
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#endif
#include <sys/resource.h>
#include <sys/time.h>
#include "utils.h"
#include "ksort.h"
#define pair64_lt(a, b) ((a).x < (b).x || ((a).x == (b).x && (a).y < (b).y))
KSORT_INIT(128, pair64_t, pair64_lt)
KSORT_INIT(64, uint64_t, ks_lt_generic)
#include "kseq.h"
KSEQ_INIT2(, gzFile, err_gzread)
/********************
* System utilities *
********************/
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) {
err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
}
return fp;
}
FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp)
{
if (freopen(fn, mode, fp) == 0) {
err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
}
return fp;
}
gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
{
gzFile fp;
if (strcmp(fn, "-") == 0) {
fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
/* According to zlib.h, this is the only reason gzdopen can fail */
if (!fp) err_fatal(func, "Out of memory");
return fp;
}
if ((fp = gzopen(fn, mode)) == 0) {
err_fatal(func, "fail to open file '%s' : %s", fn, errno ? strerror(errno) : "Out of memory");
}
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, "\n");
va_end(args);
exit(EXIT_FAILURE);
}
void err_fatal_core(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(const char *func, const char *msg)
{
fprintf(stderr, "[%s] %s\n", func, msg);
exit(EXIT_FAILURE);
}
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("fwrite", strerror(errno));
return ret;
}
size_t err_fread_noeof(void *ptr, size_t size, size_t nmemb, FILE *stream)
{
size_t ret = fread(ptr, size, nmemb, stream);
if (ret != nmemb)
{
_err_fatal_simple("fread", ferror(stream) ? strerror(errno) : "Unexpected end of file");
}
return ret;
}
int err_gzread(gzFile file, void *ptr, unsigned int len)
{
int ret = gzread(file, ptr, len);
if (ret < 0)
{
int errnum = 0;
const char *msg = gzerror(file, &errnum);
_err_fatal_simple("gzread", Z_ERRNO == errnum ? strerror(errno) : msg);
}
return ret;
}
int err_fseek(FILE *stream, long offset, int whence)
{
int ret = fseek(stream, offset, whence);
if (0 != ret)
{
_err_fatal_simple("fseek", strerror(errno));
}
return ret;
}
long err_ftell(FILE *stream)
{
long ret = ftell(stream);
if (-1 == ret)
{
_err_fatal_simple("ftell", 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("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("vfprintf", strerror(saveErrno));
return done;
}
int err_fputc(int c, FILE *stream)
{
int ret = putc(c, stream);
if (EOF == ret)
{
_err_fatal_simple("fputc", strerror(errno));
}
return ret;
}
int err_fputs(const char *s, FILE *stream)
{
int ret = fputs(s, stream);
if (EOF == ret)
{
_err_fatal_simple("fputs", strerror(errno));
}
return ret;
}
int err_puts(const char *s)
{
int ret = puts(s);
if (EOF == ret)
{
_err_fatal_simple("puts", strerror(errno));
}
return ret;
}
int err_fflush(FILE *stream)
{
int ret = fflush(stream);
if (ret != 0) _err_fatal_simple("fflush", strerror(errno));
#ifdef FSYNC_ON_FLUSH
/* Calling fflush() ensures that all the data has made it to the
kernel buffers, but this may not be sufficient for remote filesystems
(e.g. NFS, lustre) as an error may still occur while the kernel
is copying the buffered data to the file server. To be sure of
catching these errors, we need to call fsync() on the file
descriptor, but only if it is a regular file. */
{
struct stat sbuf;
if (0 != fstat(fileno(stream), &sbuf))
_err_fatal_simple("fstat", strerror(errno));
if (S_ISREG(sbuf.st_mode))
{
if (0 != fsync(fileno(stream)))
_err_fatal_simple("fsync", strerror(errno));
}
}
#endif
return ret;
}
int err_fclose(FILE *stream)
{
int ret = fclose(stream);
if (ret != 0) _err_fatal_simple("fclose", strerror(errno));
return ret;
}
int err_gzclose(gzFile file)
{
int ret = gzclose(file);
if (Z_OK != ret)
{
_err_fatal_simple("gzclose", Z_ERRNO == ret ? strerror(errno) : zError(ret));
}
return ret;
}
/*********
* Timer *
*********/
double cputime(void)
{
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(void)
{
struct timeval tp;
struct timezone tzp;
gettimeofday(&tp, &tzp);
return tp.tv_sec + tp.tv_usec * 1e-6;
}
long peakrss(void)
{
struct rusage r;
getrusage(RUSAGE_SELF, &r);
#ifdef __linux__
return r.ru_maxrss * 1024;
#else
return r.ru_maxrss;
#endif
}