int main_pad2unpad(int argc, char *argv[])
{
bamFile in, out;
if (argc == 1) {
fprintf(stderr, "Usage: samtools depad <in.bam>\n");
return 1;
}
in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
out = bam_dopen(fileno(stdout), "w");
bam_pad2unpad(in, out);
bam_close(in); bam_close(out);
return 0;
}
int main_pad2unpad(int argc, char *argv[])
{
samFile *in = 0, *out = 0;
bam_hdr_t *h = 0, *h_fix = 0;
faidx_t *fai = 0;
int c, compress_level = -1, is_long_help = 0;
char in_mode[5], out_mode[6], *fn_out = 0, *fn_list = 0;
int ret=0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 'T'),
{ NULL, 0, NULL, 0 }
};
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
while ((c = getopt_long(argc, argv, "SCso:u1T:?", lopts, NULL)) >= 0) {
switch (c) {
case 'S': break;
case 'C': hts_parse_format(&ga.out, "cram"); break;
case 's': assert(compress_level == -1); hts_parse_format(&ga.out, "sam"); break;
case 'o': fn_out = strdup(optarg); break;
case 'u':
compress_level = 0;
if (ga.out.format == unknown_format)
hts_parse_format(&ga.out, "bam");
break;
case '1':
compress_level = 1;
if (ga.out.format == unknown_format)
hts_parse_format(&ga.out, "bam");
break;
case '?': is_long_help = 1; break;
default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c);
return usage(is_long_help);
}
}
if (argc == optind) return usage(is_long_help);
strcat(out_mode, "h");
if (compress_level >= 0) {
char tmp[2];
tmp[0] = compress_level + '0'; tmp[1] = '\0';
strcat(out_mode, tmp);
}
// Load FASTA reference (also needed for SAM -> BAM if missing header)
if (ga.reference) {
fn_list = samfaipath(ga.reference);
fai = fai_load(ga.reference);
}
// open file handlers
if ((in = sam_open_format(argv[optind], in_mode, &ga.in)) == 0) {
fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
ret = 1;
goto depad_end;
}
if (fn_list && hts_set_fai_filename(in, fn_list) != 0) {
fprintf(stderr, "[depad] failed to load reference file \"%s\".\n", fn_list);
ret = 1;
goto depad_end;
}
if ((h = sam_hdr_read(in)) == 0) {
fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
ret = 1;
goto depad_end;
}
if (fai) {
h_fix = fix_header(h, fai);
} else {
fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
h_fix = h;
}
char wmode[2];
strcat(out_mode, sam_open_mode(wmode, fn_out, NULL)==0 ? wmode : "b");
if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
ret = 1;
goto depad_end;
}
// Reference-based CRAM won't work unless we also create a new reference.
// We could embed this, but for now we take the easy option.
if (ga.out.format == cram)
hts_set_opt(out, CRAM_OPT_NO_REF, 1);
if (sam_hdr_write(out, h_fix) != 0) {
fprintf(stderr, "[depad] failed to write header.\n");
ret = 1;
goto depad_end;
}
// Do the depad
ret = bam_pad2unpad(in, out, h, fai);
depad_end:
// close files, free and return
if (fai) fai_destroy(fai);
if (h) bam_hdr_destroy(h);
sam_close(in);
sam_close(out);
free(fn_list); free(fn_out);
return ret;
}