From b9d3fc3fbbac0f85df46408937cac6852cab5cd7 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 30 Mar 2010 22:40:17 +0000
Subject: [PATCH] Now checks if the i-th element of the FiltrationContext[] is
 null before trying to access it.  This seems to happen occassionally at the
 very end of a VCF file... the array will be 6 elements long, but the last
 element will actually be null.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3097 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/filters/ClusteredSnps.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
index b4935791f..7dfa6647a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
@@ -33,7 +33,7 @@ public class ClusteredSnps {
 
             int currentIndex = i;
             while ( ++currentIndex < variants.length ) {
-                if ( variants[currentIndex].getVariantContext().isVariant() ) {
+                if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) {
                     if ( ++snpsSeen == snpThreshold ) {
                         right = variants[currentIndex].getVariantContext().getLocation();
                         break;