From 7b05091c0466a3b796680d3d211ad16a971de4a9 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 13 Apr 2010 13:58:17 +0000
Subject: [PATCH] DoC now does not require a -o argument. (Change for Matt)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 3df549a43..d591abaaa 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -102,7 +102,8 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
         }
 
         if ( getToolkit().getArguments().outFileName == null ) {
-            throw new StingException("This walker requires that you specify an output file (-o)");
+            logger.warn("This walker creates many output files from one input file; you may wish to specify an input file rather "+
+                        "than defaulting all output to stdout.");
         }
 
         if ( ! omitDepthOutput ) { // print header
@@ -299,7 +300,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
 
         printIntervalTable(statsOut,nTargetsByAvgCvgBySample,firstStats.getEndpoints());
 
-        if ( ! getToolkit().getArguments().outFileName.contains("stdout")) {
+        if ( getToolkit().getArguments().outErrFileName != null && ! getToolkit().getArguments().outFileName.contains("stdout")) {
             summaryOut.close();
             statsOut.close();
         }
@@ -490,7 +491,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
 
     public File deriveFromStream(String append) {
         String name = getToolkit().getArguments().outFileName;
-        if ( name.contains("stdout") || name.contains("Stdout") || name.contains("STDOUT")) {
+        if ( name == null || name.contains("stdout") || name.contains("Stdout") || name.contains("STDOUT")) {
             return null;
         } else {
             return new File(name+"."+append);