From 591102a84134a4c6f2ed35e8ef82dac1f02bb59c Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Feb 2010 21:50:58 +0000
Subject: [PATCH] Don't close the output stream if we're printing to stdout

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2891 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/oneoffprojects/walkers/CoverageStatistics.java    | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java
index 6cc263930..5f5b96d49 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java
@@ -231,8 +231,10 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
 
         printIntervalTable(statsOut,nTargetsByAvgCvgBySample,firstStats.getEndpoints());
 
-        summaryOut.close();
-        statsOut.close();
+        if ( ! getToolkit().getArguments().outFileName.contains("stdout")) {
+            summaryOut.close();
+            statsOut.close();
+        }
 
         return firstStats;
     }