diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index f6d42afb1..613a31ed3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -311,7 +311,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                         // for each comp track
                         for ( final RodBinding<VariantContext> compRod : comps ) {
                             // no sample stratification for comps
-                            final Set<VariantContext> compSet = compVCs.get(compRod) == null ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
+                            final HashMap<String, Set<VariantContext>> compSetHash = compVCs.get(compRod);
+                            final Set<VariantContext> compSet = (compSetHash == null || compSetHash.size() == 0) ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
 
                             // find the comp
                             final VariantContext comp = findMatchingComp(eval, compSet);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index ed0e8d7f6..f31dd9f9f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -347,9 +347,9 @@ public class VariantEvalUtils {
                         }
                     }
                 }
-
-                bindings.put(track, mapping);
             }
+
+            bindings.put(track, mapping);
         }
 
         return bindings;