From a9d07725161ea72359b43054426911ec0849ecc9 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 26 Jan 2011 18:25:03 +0000
Subject: [PATCH] When evaluating JEXL expressions, on't blow up if the eval VC
 is null

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5085 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/newvarianteval/NewVariantEvalWalker.java      | 1 +
 .../walkers/newvarianteval/stratifications/JexlExpression.java | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

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);
             }
         }