From 9c0b81e946198142fc84272698a1dc763e3604fe Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 May 2009 22:09:49 +0000
Subject: [PATCH] Default flags to 'not required'.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@612 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/cmdLine/ArgumentDefinitions.java          | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
index ca473f422..bd36dc604 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
@@ -249,14 +249,14 @@ class ArgumentDefinition {
      * @param sourceField Source field for the argument, extracted from the sourceClass.
      */
     public ArgumentDefinition( Argument argument, Class sourceClass, Field sourceField ) {
+        this.sourceClass = sourceClass;
+        this.sourceField = sourceField;
+
         fullName = argument.fullName().trim().length() > 0 ? argument.fullName().trim() : sourceField.getName().toLowerCase();
         shortName = argument.shortName().trim().length() > 0 ? argument.shortName().trim() : null;
         doc = argument.doc();
-        required = argument.required();
+        required = argument.required() && !isFlag();
         exclusive = argument.exclusive().trim().length() > 0 ? argument.exclusive().trim() : null;
-
-        this.sourceClass = sourceClass;
-        this.sourceField = sourceField;
     }
 
     /**