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#include <ctype.h>
#include <assert.h>
#include <unistd.h>
#include <stdio.h>
#include "bam.h"
#include "bam_endian.h"
#include "htslib/khash.h"
#include "htslib/ksort.h"
#include "htslib/knetfile.h"
#include "pysam_util.h"
FILE * pysam_stderr = NULL;
FILE * pysam_stdout = NULL;
const char * pysam_stdout_fn = NULL;
int PYSAM_STDOUT_FILENO = STDOUT_FILENO;
FILE * pysam_set_stderr(int fd)
{
if (pysam_stderr != NULL)
fclose(pysam_stderr);
pysam_stderr = fdopen(fd, "w");
return pysam_stderr;
}
void pysam_unset_stderr(void)
{
if (pysam_stderr != NULL)
fclose(pysam_stderr);
pysam_stderr = fopen("/dev/null", "w");
}
FILE * pysam_set_stdout(int fd)
{
if (pysam_stdout != NULL)
fclose(pysam_stdout);
pysam_stdout = fdopen(fd, "w");
if (pysam_stdout == NULL)
{
fprintf(pysam_stderr, "could not set stdout to fd %i", fd);
}
PYSAM_STDOUT_FILENO = fd;
return pysam_stdout;
}
void pysam_set_stdout_fn(const char *fn)
{
pysam_stdout_fn = fn;
}
void pysam_unset_stdout(void)
{
if (pysam_stdout != NULL)
fclose(pysam_stdout);
pysam_stdout = fopen("/dev/null", "w");
PYSAM_STDOUT_FILENO = STDOUT_FILENO;
}
void set_optind(int val)
{
// setting this in cython via
// "from posix.unistd cimport optind"
// did not work.
//
// setting to 0 forces a complete re-initialization
optind = val;
}
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