From: Heng Li <lh3@live.co.uk>
Date: Sun, 13 Jun 2010 21:29:52 +0000 (+0000)
Subject: fixed a bug for unmapped sequences in indexing
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=64b94f9ab3c03cc12206d6e2a2e219ec9e2e1b17;p=samtools.git

fixed a bug for unmapped sequences in indexing
---

diff --git a/bam_index.c b/bam_index.c
index 6fffd75..7e026b3 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -178,7 +178,7 @@ bam_index_t *bam_index_core(bamFile fp)
 					bam1_qname(b), last_coor, c->pos, c->tid+1);
 			exit(1);
 		}
-		insert_offset2(&idx->index2[b->core.tid], b, last_off);
+		if (c->tid >= 0) 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);