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#include <getopt.h>
#include <unistd.h>
#include <setjmp.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "bcftools.pysam.h"
FILE * bcftools_stderr = NULL;
FILE * bcftools_stdout = NULL;
const char * bcftools_stdout_fn = NULL;
FILE * bcftools_set_stderr(int fd)
{
if (bcftools_stderr != NULL)
fclose(bcftools_stderr);
bcftools_stderr = fdopen(fd, "w");
return bcftools_stderr;
}
void bcftools_close_stderr(void)
{
fclose(bcftools_stderr);
bcftools_stderr = NULL;
}
FILE * bcftools_set_stdout(int fd)
{
if (bcftools_stdout != NULL)
fclose(bcftools_stdout);
bcftools_stdout = fdopen(fd, "w");
if (bcftools_stdout == NULL)
{
fprintf(bcftools_stderr, "could not set stdout to fd %i", fd);
}
return bcftools_stdout;
}
void bcftools_set_stdout_fn(const char *fn)
{
bcftools_stdout_fn = fn;
}
void bcftools_close_stdout(void)
{
fclose(bcftools_stdout);
bcftools_stdout = NULL;
}
int bcftools_puts(const char *s)
{
if (fputs(s, bcftools_stdout) == EOF) return EOF;
return putc('\n', bcftools_stdout);
}
static jmp_buf bcftools_jmpbuf;
static int bcftools_status = 0;
int bcftools_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(bcftools_jmpbuf) == 0)
return bcftools_main(argc, argv);
else
return bcftools_status;
}
void bcftools_exit(int status)
{
bcftools_status = status;
longjmp(bcftools_jmpbuf, 1);
}
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