From 7c6455fe367f7f071b260770779037bb81054d1b Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 29 Mar 2009 01:50:27 +0000
Subject: [PATCH] Handle the case where a walker is being run outside of the
 GATK framework, such as JUnit tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@222 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/walkers/Walker.java    | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index 4dc0e55f4..55be26501 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -25,9 +25,15 @@ public abstract class Walker<MapType, ReduceType> {
     protected PrintStream err = null;
 
     protected Walker() {
-        GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
-        out = GenomeAnalysisTK.Instance.out;
-        err = GenomeAnalysisTK.Instance.err;
+	if( GenomeAnalysisTK.Instance != null ) {
+	    GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
+	    out = GenomeAnalysisTK.Instance.out;
+	    err = GenomeAnalysisTK.Instance.err;
+	}
+	else {
+	    out = System.out;
+	    err = System.err;
+	}
     }
 
     /**