X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_index.c;h=9610a2656031657b796abc68bf32c1b6f1564745;hb=cb5f44947629a68d16a48d32eef6e42a66e482fe;hp=9b71bdbac9167ec38719be411ee6d42a276c927f;hpb=4d48006473298b62ee54f13d706f9f2e512e02bd;p=samtools.git

diff --git a/bam_index.c b/bam_index.c
index 9b71bdb..9610a26 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -176,7 +176,7 @@ bam_index_t *bam_index_core(bamFile fp)
 	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) {
@@ -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);