From ee777c89de68a726f4247d8d72ab61e56b18821e Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 May 2009 18:43:00 +0000
Subject: [PATCH] Change the default mechanism for adding ROD bindings to the
 new system.  TODO: create a new object type for these triplets.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@642 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 7b57058c6..084f49c28 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -171,9 +171,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      */
     private void bindConvenienceRods(final String name, final String type, final String file )
     {
-        ROD_BINDINGS.add(name);
-        ROD_BINDINGS.add(type);
-        ROD_BINDINGS.add(file);
+        ROD_BINDINGS.add( Utils.join(",", new String[] { name, type, file }) );
     }
 
     private static void printExitSystemMsg(final String msg) {