* samtools-0.1.3-9 (r256)

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 60a194525425d711a23a286d6f411358911173f1..482f33ca5bbfec2af6162518d21936e86105c058 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -142,13 +142,14 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
        }
        for (i = n = 0; i < _n; ++i) {
                const bam_pileup1_t *p = pl + i;
-               uint32_t q, x = 0;
+               uint32_t q, x = 0, qq;
                if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
                q = (uint32_t)bam1_qual(p->b)[p->qpos];
                x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
                if (p->b->core.qual < q) q = p->b->core.qual;
                x |= q << 24;
-               q = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+               qq = bam1_seqi(bam1_seq(p->b), p->qpos);
+               q = bam_nt16_nt4_table[qq? qq : ref_base];
                if (!p->is_del && q < 4) x |= 1 << 21 | q << 16;
                bm->aux->info[n++] = x;
        }