* samtools-0.1.6-21 (r508)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index fff42f7c582b0f40947616723e3c3fc15ca630c9..e2601ecc3c26b41051d0148a9cf9696036d297fb 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -182,7 +182,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
        // call the consensus and indel
        if (d->format & BAM_PLF_CNS) // call consensus
                cns = bam_maqcns_call(n, pu, d->c);
-       if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { // call indels
+       if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
                if (proposed_indels) // the first element gives the size of the array
                        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);