off_beg = off_end = bam_tell(fp);
while ((ret = bam_read1(fp, b)) >= 0) {
if (c->tid < 0) ++n_no_coor;
- if (last_tid < c->tid) { // change of chromosomes
+ if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
last_tid = c->tid;
last_bin = 0xffffffffu;
- } else if (last_tid > c->tid) {
+ } else if ((uint32_t)last_tid > (uint32_t)c->tid) {
fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
bam1_qname(b), last_tid+1, c->tid+1);
return NULL;
- } else if (last_coor > c->pos) {
+ } else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
bam1_qname(b), last_coor, c->pos, c->tid+1);
return NULL;