From 8c08f479232eee50d41a70f852ac52734f773a03 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 11 Aug 2010 20:32:22 +0000
Subject: [PATCH] 1) Make sure that the table size is set correctly in
 finalize() 2) Make sure variants are biallelic before asking for
 isTransversion()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4016 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/varianteval/SimpleMetricsBySample.java              | 2 +-
 .../walkers/varianteval/VariantEvaluatorBySample.java           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
index c6ee2e44e..14ad75aa3 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
@@ -78,7 +78,7 @@ class TiTvRatioSample extends SampleDataPoint {
     }
 
     public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( vc != null && vc.isSNP() ) {
+        if ( vc != null && vc.isSNP() && vc.isBiallelic() ) {
             if ( VariantContextUtils.isTransition(vc) ) {
                 nTi++;
             } else {
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
index 8a7bfb18b..cd64beb37 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
@@ -163,7 +163,7 @@ class EvalBySample implements TableType {
     }
 
     public void finalizeTable() {
-        finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.size()];
+        finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.firstEntry().getValue().size()];
         int i = 0;
         for ( Map.Entry<String,List<SampleDataPoint>> evalBySample : sampleAndEvalResults.entrySet() ) {
             int j = 0;