* samtools-0.1.9-8 (r809)

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 1ba288ccd949e3b506b7c786f8f609480af05cb2..8537e232191189ee489ba7ce681008c12a39b829 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -124,7 +124,10 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
                if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
                        call->unseen = j, call->a[j++] = qsum[i]&3;
                call->n_alleles = j;
-       } else call->n_alleles = j;
+       } else {
+               call->n_alleles = j;
+               if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+       }
        // set the PL array
        if (call->n < n) {
                call->n = n;