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 implements TreeR private String getReferenceOrderedData( RefMetaDataTracker tracker ) { ArrayList rodStrings = new ArrayList(); 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 } }