From a5006831d7b52748a77aa86512979d220c9540a7 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 28 Sep 2011 11:35:52 -0400
Subject: [PATCH] Shows "" not empty space when default string value is ""

---
 .../sting/utils/help/GenericDocumentationHandler.java    | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index b100b3e1b..20f9eccd3 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -325,11 +325,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
                 return Arrays.toString((Object[])value);
             else
                 throw new RuntimeException("Unexpected array type in prettyPrintValue.  Value was " + value + " type is " + type);
-        } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) )
+        } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) ) {
             // annoying special case to handle the UnBound() constructor
             return "none";
-
-        return value.toString();
+        } else if ( value instanceof String ) {
+            return value.equals("") ? "\"\"" : value;
+        } else {
+            return value.toString();
+        }
     }
 
     /**