From 355136928e0b01f2eab9cfdc8e96b9ef565b15f3 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Sep 2009 18:55:08 +0000
Subject: [PATCH] Play nice with other jobs in this VM -- don't close stdout /
 stderr.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1646 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/io/storage/OutputStreamStorage.java           | 5 +++++
 .../broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
index 8f71eaa57..002951b99 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
@@ -87,6 +87,11 @@ public class OutputStreamStorage extends OutputStream implements Storage<OutputS
      * @{inheritDoc}
      */
     public void close() {
+        // Don't close System.out or System.err; this'll cause trouble
+        // with subsequent code running in this VM.
+        if( outputStream == System.out || outputStream == System.err )
+            return;
+        
         try {
             outputStream.close();
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
index 5722d6ca2..5cf84c5a2 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
@@ -105,7 +105,7 @@ public class OutputStreamStub extends OutputStream implements Stub<OutputStream>
      * @{inheritDoc}
      */
     public void flush() throws IOException {
-        outputTracker.getStorage(this).close();
+        outputTracker.getStorage(this).flush();
     }
 
     /**