int main_samview(int argc, char *argv[])
{
- int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, is_hex = 0;
samfile_t *in = 0, *out = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:x")) >= 0) {
switch (c) {
case 'S': is_bamin = 0; break;
case 'b': is_bamout = 1; break;
case 'u': is_uncompressed = 1; break;
case 'l': g_library = strdup(optarg); break;
case 'r': g_rg = strdup(optarg); break;
+ case 'x': is_hex = 1; break;
default: return usage();
}
}
if (is_bamin) strcat(in_mode, "b");
if (is_header) strcat(out_mode, "h");
if (is_uncompressed) strcat(out_mode, "u");
+ if (is_hex && !is_bamout) strcat(out_mode, "x");
if (argc == optind) return usage();
// open file handlers
fprintf(stderr, " -H print header only (no alignments)\n");
fprintf(stderr, " -S input is SAM\n");
fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
+ fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n");
fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");