X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_index.c;h=9610a2656031657b796abc68bf32c1b6f1564745;hp=66d8eb8a896ab5a0a4decf612e65eac158e92cbf;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=b301e959d73eee0955c57004f344f17af00703f4

diff --git a/bam_index.c b/bam_index.c
index 66d8eb8..9610a26 100644
--- 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);