From 9cdc341be58cde5845333160a8fa2a61961b204e Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 24 Nov 2010 01:45:44 +0000
Subject: [PATCH] Trivial update for data processing paper: change syntax of
 output argument for Beagle by depth walker to update to new GATK format.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4724 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffprojects/walkers/BeagleOutputByDepthWalker.java   | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
index a263008fc..5242125db 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
@@ -54,10 +54,8 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
     public static final String INPUT_COMP_ROD_NAME = "comp";
 
     @Output
-    public PrintStream out;
+    protected PrintStream outputWriter = null;
 
-    @Argument(fullName = "output_file", shortName = "output", doc = "File to output results", required = true)
-    public PrintStream outputWriter = null;
 
     public void initialize() {
 
@@ -211,7 +209,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
      * @param result  the number of loci seen.
      */
     public void onTraversalDone(Integer result) {
-        out.printf("Processed %d loci.\n", result);
+        System.out.printf("Processed %d loci.\n", result);
 
     }