From 17758b381c973c1ffd5483f7809e08c30425f225 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Sep 2009 19:47:43 +0000
Subject: [PATCH] Properly initialize redirected output streams in case of out
 and err.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1629 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/io/OutputTracker.java            | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index 82c587d73..87fe2c2a9 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -10,6 +10,7 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
 import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.io.storage.OutputStreamStorage;
 
 import java.io.*;
 import java.lang.reflect.Field;
@@ -65,16 +66,16 @@ public abstract class OutputTracker {
         // Otherwise, initialize them separately.
         if( outFileName != null && outFileName.equals(errFileName) ) {
             outStub = errStub = new OutputStreamStub(new File(outFileName));
-            addOutput(outStub);
+            addOutput(outStub,new OutputStreamStorage(outStub));
         }
         else {
             outStub = (outFileName != null) ? new OutputStreamStub(new File(outFileName))
                                             : new OutputStreamStub(System.out);
-            addOutput(outStub);
+            addOutput(outStub,new OutputStreamStorage(outStub));
 
             errStub = (errFileName != null) ? new OutputStreamStub(new File(errFileName))
                                             : new OutputStreamStub(System.err);
-            addOutput(errStub);
+            addOutput(errStub,new OutputStreamStorage(outStub));
         }
     }
 
@@ -120,8 +121,16 @@ public abstract class OutputTracker {
      * @param stub Stream to manage.
      */
     public <T> void addOutput(Stub<T> stub) {
+        addOutput(stub,null);
+    }
+
+    /**
+     * Provide a mechanism for injecting supplemental streams for external management.
+     * @param stub Stream to manage.
+     */
+    public <T> void addOutput(Stub<T> stub, Storage<T> storage) {
         stub.register(this);
-        outputs.put(stub,null);
+        outputs.put(stub,storage);        
     }
 
     /**