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#include <getopt.h>
#include <unistd.h>
#include <setjmp.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "samtools.pysam.h"
FILE * samtools_stderr = NULL;
FILE * samtools_stdout = NULL;
const char * samtools_stdout_fn = NULL;
FILE * samtools_set_stderr(int fd)
{
if (samtools_stderr != NULL)
fclose(samtools_stderr);
samtools_stderr = fdopen(fd, "w");
return samtools_stderr;
}
void samtools_close_stderr(void)
{
fclose(samtools_stderr);
samtools_stderr = NULL;
}
FILE * samtools_set_stdout(int fd)
{
if (samtools_stdout != NULL)
fclose(samtools_stdout);
samtools_stdout = fdopen(fd, "w");
if (samtools_stdout == NULL)
{
fprintf(samtools_stderr, "could not set stdout to fd %i", fd);
}
return samtools_stdout;
}
void samtools_set_stdout_fn(const char *fn)
{
samtools_stdout_fn = fn;
}
void samtools_close_stdout(void)
{
fclose(samtools_stdout);
samtools_stdout = NULL;
}
int samtools_puts(const char *s)
{
if (fputs(s, samtools_stdout) == EOF) return EOF;
return putc('\n', samtools_stdout);
}
static jmp_buf samtools_jmpbuf;
static int samtools_status = 0;
int samtools_dispatch(int argc, char *argv[])
{
/* Reset getopt()/getopt_long() processing. */
#if defined __GLIBC__
optind = 0;
#elif defined _OPTRESET || defined _OPTRESET_DECLARED
optreset = optind = 1;
#else
optind = 1;
#endif
if (setjmp(samtools_jmpbuf) == 0)
return samtools_main(argc, argv);
else
return samtools_status;
}
void samtools_exit(int status)
{
samtools_status = status;
longjmp(samtools_jmpbuf, 1);
}
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