From 72e030a6707d3ece8f5820c15fe4954df8b4af06 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 6 May 2010 22:33:00 +0000
Subject: [PATCH] require that snps be biallelic before we pass them to the
 TiTv calculation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/varianteval/SimpleMetricsByAC.java        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
index 15acb7399..1766badb9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
@@ -143,6 +143,7 @@ public class SimpleMetricsByAC extends VariantEvaluator {
 
         if (eval != null &&
                 eval.isSNP() &&
+                eval.isBiallelic() &&
                 eval.hasGenotypes()) {
             if ( metrics == null )
                 metrics = new MetricsByAc(2 * eval.getNSamples());