From 18ed9547411cc0ab62a01446f144039d28af3c26 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 5 Jan 2012 15:33:26 -0500
Subject: [PATCH] Compute Ti/Tv only if bi-allelic

---
 .../gatk/walkers/varianteval/evaluators/VariantSummary.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
index a271d3c35..b3f3630bd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
@@ -224,7 +224,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
         allVariantCounts.inc(type, ALL);
 
         // type specific calculations
-        if ( type == Type.SNP ) {
+        if ( type == Type.SNP && eval.isBiallelic() ) {
             titvTable = VariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample;
             titvTable.inc(type, ALL);
         }