bam_header_t *out_header = sam_header_read2(chr_list);
refmap.clear();
for (int i = 0; i < out_header->n_targets; i++) {
bam_header_t *out_header = sam_header_read2(chr_list);
refmap.clear();
for (int i = 0; i < out_header->n_targets; i++) {
// at least one segment is not properly mapped
if ((b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004))) continue;
// at least one segment is not properly mapped
if ((b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004))) continue;