From c3dbbe7f91b210ff5b8bda9870e97c6ba872143f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 21 Jan 2011 04:59:28 +0000
Subject: [PATCH] Bug fix: don't assume users won't use arbitrary rods on the
 commandline

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5040 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index 69d7243c8..e955155c6 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -149,7 +149,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
     private String getReferenceOrderedData( RefMetaDataTracker tracker ) {
         ArrayList<String> rodStrings = new ArrayList<String>();
         for ( GATKFeature datum : tracker.getAllRods() ) {
-            if ( datum != null && ! (datum.getUnderlyingObject() instanceof DbSNPFeature)) {
+            if ( datum != null && datum.getUnderlyingObject() instanceof ReferenceOrderedDatum ) {
                 rodStrings.add(((ReferenceOrderedDatum)datum.getUnderlyingObject()).toSimpleString()); // TODO: Aaron: this line still survives, try to remove it
             }
         }