From 31ee8aa01a6b752f5a22af226682950424003890 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 21 Jun 2012 09:54:36 -0400
Subject: [PATCH] JEXL update

-- Update to 2.1.1 from 2.0
-- VariantFiltrationWalker now allows you to run with type unsafe selects, which all default to false when matching.  So "AF < 0.5" works even in the presence of multi-allelics now.
--
---
 ivy.xml                                                      | 2 +-
 .../sting/utils/variantcontext/VariantContextUtils.java      | 5 +++--
 .../sting/utils/variantcontext/VariantJEXLContext.java       | 4 +++-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/ivy.xml b/ivy.xml
index 9cc92d890..f76880b94 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -59,7 +59,7 @@
      
     <!-- Commons Dependencies -->  
     <dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
-    <dependency org="org.apache.commons" name="commons-jexl" rev="2.0"/>
+    <dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
     <dependency org="commons-lang" name="commons-lang" rev="2.5"/>
     <dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
     <dependency org="commons-io" name="commons-io" rev="2.1"/>
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 099c3d541..e2c30913f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -52,8 +52,9 @@ public class VariantContextUtils {
     private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false;
 
     static {
-        engine.setSilent(false); // will throw errors now for selects that don't evaluate properly
-        engine.setLenient(false);
+        engine.setSilent(true); // will throw errors now for selects that don't evaluate properly
+        engine.setLenient(true);
+        engine.setDebug(false);
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
index 6ecb898df..e25599812 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
@@ -264,7 +264,9 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
         // if the context is null, we need to create it to evaluate the JEXL expression
         if (this.jContext == null) createContext();
         try {
-            jexl.put (exp, (Boolean) exp.exp.evaluate(jContext));
+            final Boolean value = (Boolean) exp.exp.evaluate(jContext);
+            // treat errors as no match
+            jexl.put(exp, value == null ? false : value);
         } catch (Exception e) {
             throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
         }