From 376bc563d45c97e805f6c460db5dbdb0bd321baa Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 22 Dec 2010 22:39:09 +0000
Subject: [PATCH] Trivial change to allow GenerateVariantClusters to be run on
 indels - not that VQSR now works on indels, far from it, but at least it's a
 first step and it allows us to generate cluster plots to see how well
 known/novel sites differentiate in their covariates (short answer: no
 difference/separation :( ).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4902 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 81995f5ac..9818e6058 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -179,7 +179,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
         final double annotationValues[] = new double[annotationKeys.size()];
 
         for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) {
-            if( vc != null && vc.isSNP() ) {
+            if( vc != null  ) {
                 if( !vc.isFiltered() || IGNORE_ALL_INPUT_FILTERS || (ignoreInputFilterSet != null && ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
                     int iii = 0;
                     for( final String key : annotationKeys ) {