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;
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);