diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 436376bfa..c745663c3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -115,9 +115,15 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
 
     @Argument(shortName="select", doc="One or more stratifications to use when evaluating the data", required=false)
     protected String[] SELECT_EXPS = {};
-
+    //protected String[] SELECT_EXPS = {"set == \"Intersection\"",
+    //        "set == \"HiSeq.WGS.cleaned.ug.vcf\"",
+    //        "set == \"HiSeq.WGS.cleaned.ug.vcf\" || set == \"Intersection\"",
+    //        "set == \"HiSeq.WGS.raw.OQ.ug.vcf\"",
+    //        "set == \"HiSeq.WGS.raw.OQ.ug.vcf\" || set == \"Intersection\""};
+    
     @Argument(shortName="selectName", doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)", required=false)
     protected String[] SELECT_NAMES = {};
+    //protected String[] SELECT_NAMES = {"Intersection", "x1", "x2", "x3", "x4"};
 
     @Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false)
     protected String[] KNOWN_NAMES = {DbSNPHelper.STANDARD_DBSNP_TRACK_NAME};
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
index 8954ab45b..8bd27d389 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
@@ -133,9 +133,11 @@ public class AminoAcidTransition extends VariantEvaluator {
     public AminoAcidTransition(VariantEvalWalker parent) {
         super(parent);
         enabled = parent.aminoAcidTransitionKey != null;
-        getParsingInformation(parent);
-        lookup = new AminoAcidTable();
-        acidTable = new AminoAcidTiTvTable();
+        if ( enabled ) {
+            getParsingInformation(parent);
+            lookup = new AminoAcidTable();
+            acidTable = new AminoAcidTiTvTable();
+        }
     }
 
     private void getParsingInformation(VariantEvalWalker parent) {
@@ -172,6 +174,7 @@ public class AminoAcidTransition extends VariantEvaluator {
     public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         String interesting = null;
         if ( eval != null && eval.hasAttribute(infoKey) ) {
+	    //if ( enabled && eval != null && eval.hasAttribute(infoKey) ) {
             String[] parsedNames = ( (String) eval.getAttribute(infoKey)).split(infoValueSplit);
             String first = "none";
             String second = "none";