*/
r_tid = b->core.tid;
unpad_seq(b, &r);
+ if (h->target_len[r_tid] != r.l) {
+ fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %i in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+ return -1;
+ }
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap = realloc(posmap, r.m * sizeof(int));