bam_header_t *h;
bam1_t *b;
kstring_t r, q;
- int r_tid = -1;
+ int r_tid = -1;
uint32_t *cigar2 = 0;
int n2 = 0, m2 = 0, *posmap = 0;
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);
+ fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld 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));