diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
index 4cb5d3d72..60f4e371a 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
@@ -461,6 +461,7 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
      * @param trackNames      the list of track names to process
      * @param sampleNames     the list of samples to include
      * @param allowableTypes  a set of allowable variation types
+     * @param byFilter        if false, only accept PASSing VariantContexts.  Otherwise, accept both PASSing and filtered sites
      * @return  a mapping of track names to a list of VariantContext objects
      */
     private HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, Set<String> sampleNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java
index ffffdaaae..b521d65ce 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/stratifications/JexlExpression.java
@@ -32,8 +32,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
         relevantStates.add("none");
 
         for ( VariantContextUtils.JexlVCMatchExp jexlExpression : jexlExpressions ) {
-            System.out.println(jexlExpression.name + " " + jexlExpression.exp.getExpression());
-            if (VariantContextUtils.match(eval, jexlExpression)) {
+            if (eval != null && VariantContextUtils.match(eval, jexlExpression)) {
                 relevantStates.add(jexlExpression.name);
             }
         }