From 07945040f8de79257da130f3cf0df86b91516492 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 4 Jul 2010 18:11:19 +0000
Subject: [PATCH] Set VariantFiltration's JEXL engine to silent for warning
 messages

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3716 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/filters/VariantFiltrationWalker.java     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 72c8457dc..a2382738b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -120,6 +120,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 
         filterExps = VariantContextUtils.initializeMatchExps(FILTER_NAMES, FILTER_EXPS);
         genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
+
+        VariantContextUtils.engine.setSilent(true);
     }
 
     public Integer reduceInit() { return 0; }