From 16c2ea4673e3fb112e88ff18294940df7751f633 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Apr 2009 15:58:57 +0000
Subject: [PATCH] Invalid arguments are not always flagged when stopAtNonOption
 is false.  Make sure stopAnNonOption is true when we do final argument
 validation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@245 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index bb158111e..0cef2b4f7 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -276,7 +276,7 @@ public class ArgumentParser {
         Collection<Option> opts = m_options.getOptions();
 
         try {
-            parser.parse(m_options, args, false);
+            parser.parse(m_options, args, !allowIncomplete);
         }
         catch( ParseException e ) {
             boolean isIncomplete = e instanceof MissingArgumentException ||