- if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
- if (g_library) {
- const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
- return (p && strcmp(p, g_library) == 0)? 0 : 1;
- } return 1;
- } else return 1;
- } else return 0;
+ if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
+ if (g_rghash) {
+ khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
+ return (k != kh_end(g_rghash))? 0 : 1;
+ }
+ }
+ }
+ if (g_library) {
+ const char *p = bam_get_library((bam_header_t*)h, b);
+ return (p && strcmp(p, g_library) == 0)? 0 : 1;
+ }
+ return 0;
+}
+
+static char *drop_rg(char *hdtxt, rghash_t h, int *len)
+{
+ char *p = hdtxt, *q, *r, *s;
+ kstring_t str;
+ memset(&str, 0, sizeof(kstring_t));
+ while (1) {
+ int toprint = 0;
+ q = strchr(p, '\n');
+ if (q == 0) q = p + strlen(p);
+ if (q - p < 3) break; // the line is too short; then stop
+ if (strncmp(p, "@RG\t", 4) == 0) {
+ int c;
+ khint_t k;
+ if ((r = strstr(p, "\tID:")) != 0) {
+ r += 4;
+ for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
+ c = *s; *s = '\0';
+ k = kh_get(rg, h, r);
+ *s = c;
+ if (k != kh_end(h)) toprint = 1;
+ }
+ } else toprint = 1;
+ if (toprint) {
+ kputsn(p, q - p, &str); kputc('\n', &str);
+ }
+ p = q + 1;
+ }
+ *len = str.l;
+ return str.s;