From 2f3ab53888950dd0ef567a11ff39ef4854b76490 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 7 May 2009 13:37:19 +0000
Subject: [PATCH] Oops.  Arguments didn't load into applications with
 non-plugins (basically everything except the GATK).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/cmdLine/CommandLineProgram.java   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
index 5a216e72b..495229f3c 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
@@ -151,6 +151,7 @@ public abstract class CommandLineProgram {
             else {
                 parser.parse(args);
                 parser.validate();
+                parser.loadArgumentsIntoObject( clp );
             }
 
             // if we're in debug mode, set the mode up