bam1_core_t *c;
uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
+ h = bam_header_read(fp);
+ if(h == 0) {
+ fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+ return NULL;
+ }
+
idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
b = (bam1_t*)calloc(1, sizeof(bam1_t));
- h = bam_header_read(fp);
c = &b->core;
idx->n = h->n_targets;
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 ((uint32_t)last_tid > (uint32_t)c->tid) {
bam1_qname(b), last_coor, c->pos, c->tid+1);
return NULL;
}
- if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
if (c->bin != last_bin) { // then possibly write the binning index
if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
insert_offset(idx->index[save_tid], save_bin, save_off, last_off);