From 7ee792df0421012a66f95432fd34f0dbd7551619 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Apr 2009 15:16:49 +0000
Subject: [PATCH] Print correct help if core arguments (--input-file et al)
 aren't correctly specified.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@244 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/cmdLine/ArgumentParser.java        | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index 9c69a7c36..bb158111e 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -269,17 +269,21 @@ public class ArgumentParser {
      * exit the program
      *
      * @param args the command line arguments we recieved
+     * @param args whether to allow incomplete command-line arguments
      */
-    public void processArgs(String[] args, boolean allowUnrecognized) throws ParseException {
+    public void processArgs(String[] args, boolean allowIncomplete) throws ParseException {
         OurPosixParser parser = new OurPosixParser();
         Collection<Option> opts = m_options.getOptions();
 
         try {
-            parser.parse(m_options, args, !allowUnrecognized);
+            parser.parse(m_options, args, false);
         }
-        catch (UnrecognizedOptionException e) {
-            // we don't care about unknown exceptions right now
-            if(!allowUnrecognized) {
+        catch( ParseException e ) {
+            boolean isIncomplete = e instanceof MissingArgumentException ||
+                                   e instanceof MissingOptionException ||
+                                   e instanceof UnrecognizedOptionException;
+
+            if( !(allowIncomplete && isIncomplete) ) {
                 logger.warn(e.getMessage());
                 throw e;
             }