X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=ba787a98bd78726503f48af1fd16582d89a357dd;hb=ec5db8370dc97a853d6fada24ec518756a35e070;hp=e2601ecc3c26b41051d0148a9cf9696036d297fb;hpb=a7dfcd368cda94d5847d3f2b42d4288399d77835;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e2601ec..ba787a9 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -121,9 +121,11 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
 	g3->offset = pos - d->last_pos;
 	d->last_pos = pos;
 	glf3_write1(d->fp_glf, g3);
-	if (proposed_indels)
-		r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
-	else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+	if (pos < d->len) {
+		if (proposed_indels)
+			r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+		else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+	}
 	if (r) { // then write indel line
 		int het = 3 * n, min;
 		min = het;