+int sam_header_parse_rg(bam_header_t *h)
+{
+ kstring_t *rgid, *rglib;
+ char *p, *q, *s, *r;
+ int n = 0;
+
+ // free
+ if (h == 0) return 0;
+ bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
+ if (h->l_text < 3) return 0;
+ // parse @RG lines
+ h->rg2lib = bam_strmap_init();
+ rgid = calloc(1, sizeof(kstring_t));
+ rglib = calloc(1, sizeof(kstring_t));
+ s = h->text;
+ while ((s = strstr(s, "@RG")) != 0) {
+ if (rgid->l && rglib->l) {
+ bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
+ ++n;
+ }
+ rgid->l = rglib->l = 0;
+ s += 3;
+ r = s;
+ if ((p = strstr(s, "ID:")) != 0) {
+ q = p + 3;
+ for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+ kputsn(q, p - q, rgid);
+ } else {
+ fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
+ break;
+ }
+ if (r < p) r = p;
+ if ((p = strstr(s, "LB:")) != 0) {
+ q = p + 3;
+ for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+ kputsn(q, p - q, rglib);
+ } else {
+ fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
+ break;
+ }
+ if (r < p) r = p;
+ s = r + 3;
+ }
+ if (rgid->l && rglib->l) {
+ bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
+ ++n;
+ }
+ free(rgid->s); free(rgid);
+ free(rglib->s); free(rglib);
+ if (n == 0) {
+ bam_strmap_destroy(h->rg2lib);
+ h->rg2lib = 0;
+ }
+ return n;
+}
+