+ if (fai) {
+ // Check the embedded reference matches the FASTA file
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) return -1;
+ assert(r.l == q.l);
+ int i;
+ for (i = 0; i < r.l; ++i) {
+ if (r.s[i] != q.s[i]) {
+ // Show gaps as ASCII 45
+ fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+ h->target_name[b->core.tid], i+1,
+ r.s[i] ? bam_nt16_rev_table[r.s[i]] : 45,
+ q.s[i] ? bam_nt16_rev_table[q.s[i]] : 45);
+ return -1;
+ }
+ }
+ }