From f42b75da7204d257b679ef027a90804c289ae0e5 Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 14:34:08 +0000
Subject: [PATCH] restore GFF_OUTPUT_FILE to a required argument.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@255 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/AlleleFrequencyWalker.java          | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
index 7af695b56..2284b0a84 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -19,9 +19,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
 {
     @Argument public int    N;
     @Argument public int    DOWNSAMPLE;
-    @Argument(required=false,defaultValue="")
-    public String GFF_OUTPUT_FILE;
-
+    @Argument public String GFF_OUTPUT_FILE;
 
     protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class);
 
@@ -457,10 +455,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         try
         {
             this.random = new java.util.Random(0);
-            if ( GFF_OUTPUT_FILE == null )
-                this.output = out;
-            else
-                this.output = new PrintStream(GFF_OUTPUT_FILE);
+            this.output = new PrintStream(GFF_OUTPUT_FILE);
         }
         catch (Exception e)
         {
@@ -480,8 +475,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         try
         {
 	        this.output.flush();
-            if ( GFF_OUTPUT_FILE != null )
-                this.output.close();
+            this.output.close();
         }
         catch (Exception e)
         {