From 4c5f640eb756f385f33e5811ffcccaab291f8392 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 29 Apr 2009 14:36:27 +0000
Subject: [PATCH] Tweak the arguments passed to the command-line arguments
 parser so that it fails less often for invalid arguments.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@560 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 c88b7d235..baba87ea0 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -280,7 +280,7 @@ public class ArgumentParser {
         OurPosixParser parser = new OurPosixParser();
 
         try {
-            parser.parse(m_options, args, !allowIncomplete);
+            parser.parse(m_options, args, false);
         }
         catch( ParseException e ) {
             boolean isIncomplete = e instanceof MissingArgumentException ||