From 3cad580655a7d4423f61504910ee457fd49db54f Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 20 May 2009 19:17:16 +0000
Subject: [PATCH] Catch and rethrow the walker's required argument, so that
 command-line arguments will be displayed when the GATK throws an argument
 exception.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@765 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/CommandLineGATK.java    | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 5d39465ee..20fbeb59a 100755
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
 
 import java.io.FileNotFoundException;
 import java.io.File;
@@ -93,7 +94,12 @@ public class CommandLineGATK extends CommandLineProgram {
         this.argCollection.analysisName = this.analysisName;
         try {
             GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
-        } catch (StingException exp) {
+        }
+        catch (ArgumentException ex) {
+            // Rethrow argument exceptions.  Let the command-line argument do what it's designed to do.
+            throw ex;            
+        }
+        catch (StingException exp) {
             System.err.println("Caught StingException. It's message is " + exp.getMessage());
             exp.printStackTrace();
             return -1;