From b434c1c240f212e807d30f9e2d90d6f7f22d6b29 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Nov 2009 03:12:20 +0000
Subject: [PATCH] Check for null entries before adding

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2099 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/varianteval/ChipConcordance.java           | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java
index 1049786ba..1c0f31d25 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java
@@ -125,8 +125,10 @@ public abstract class ChipConcordance extends BasicVariantAnalysis {
 
         // now we can finally update our truth tables with the truth vs. calls data
         for (int i = 0; i < truthTables.length; i++) {
-            ConcordanceTruthTable table = truthTables[i];
-            table.addEntry(chipEvals[i], eval, ref);
+            if ( chipEvals[i] != null ) {
+                ConcordanceTruthTable table = truthTables[i];
+                table.addEntry(chipEvals[i], eval, ref);
+            }
         }
     }