1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
|
#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);
}
|
