int main_reheader(int argc, char *argv[])
{
bam_header_t *h;
BGZF *in;
if (argc != 3) {
fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
return 1;
}
{ // read the header
tamFile fph = sam_open(argv[1]);
if (fph == 0) {
fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
return 1;
}
h = sam_header_read(fph);
sam_close(fph);
}
in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
if (in == 0) {
fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
return 1;
}
bam_reheader(in, h, fileno(stdout));
bgzf_close(in);
return 0;
}
int main_reheader(int argc, char *argv[])
{
int inplace = 0, r, add_PG = 1, c;
bam_hdr_t *h;
samFile *in;
char *arg_list = stringify_argv(argc+1, argv-1);
static const struct option lopts[] = {
{"help", no_argument, NULL, 'h'},
{"in-place", no_argument, NULL, 'i'},
{"no-PG", no_argument, NULL, 'P'},
{NULL, 0, NULL, 0}
};
while ((c = getopt_long(argc, argv, "hiP", lopts, NULL)) >= 0) {
switch (c) {
case 'P': add_PG = 0; break;
case 'i': inplace = 1; break;
case 'h': usage(stdout, 0); break;
default:
fprintf(stderr, "Invalid option '%c'\n", c);
usage(stderr, 1);
}
}
if (argc - optind != 2)
usage(stderr, 1);
{ // read the header
samFile *fph = sam_open(argv[optind], "r");
if (fph == 0) {
fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[optind]);
return 1;
}
h = sam_hdr_read(fph);
sam_close(fph);
if (h == NULL) {
fprintf(stderr, "[%s] failed to read the header for '%s'.\n",
__func__, argv[1]);
return 1;
}
}
in = sam_open(argv[optind+1], inplace?"r+":"r");
if (in == 0) {
fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[optind+1]);
return 1;
}
if (hts_get_format(in)->format == bam) {
r = bam_reheader(in->fp.bgzf, h, fileno(stdout), arg_list, add_PG);
} else {
if (inplace)
r = cram_reheader_inplace(in->fp.cram, h, arg_list, add_PG);
else
r = cram_reheader(in->fp.cram, h, arg_list, add_PG);
}
if (sam_close(in) != 0)
r = -1;
bam_hdr_destroy(h);
if (arg_list)
free(arg_list);
return -r;
}