diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
index 640cff2ba..29b649afe 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
@@ -2,16 +2,18 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.io.PrintStream;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -23,6 +25,9 @@ public class CountIntervals extends RefWalker<Long, Long> {
     @Output
     PrintStream out;
 
+    @Input(fullName="check", shortName = "check", doc="Any number of RODs", required=false)
+    public List<RodBinding<Feature>> features = Collections.emptyList();
+
     @Argument(fullName="numOverlaps",shortName="no",doc="Count all occurrences of X or more overlapping intervals; defaults to 2", required=false)
     int numOverlaps = 2;
 
@@ -37,7 +42,7 @@ public class CountIntervals extends RefWalker<Long, Long> {
             return null;
         }
 
-        List<Feature> checkIntervals = tracker.getValues(Feature.class, "check");
+        List<Feature> checkIntervals = tracker.getValues(features);
         return (long) checkIntervals.size();
     }