From a1218ef50869ada7ac06686ff9651652fe48d0c3 Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 2 Jun 2009 19:32:29 +0000
Subject: [PATCH] changed default value for failure output

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@880 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/SomaticMutationWalker.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
index 56b4f7372..e72199b8f 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
@@ -75,8 +75,8 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
     public int MIN_MUTANT_SUM = 100;
 
 
-    @Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
-    public boolean OUTPUT_FAILURES = false;
+//    @Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
+    public boolean OUTPUT_FAILURES = true;
 
 
     public boolean bedOutput = true;