Starting the work on next package update.

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 66d8eb8a896ab5a0a4decf612e65eac158e92cbf..9610a2656031657b796abc68bf32c1b6f1564745 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -188,7 +188,7 @@ bam_index_t *bam_index_core(bamFile fp)
                                        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);