From a3d2764d11ce75cbc5258054eb7c547e2c0981a2 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 17 Aug 2012 10:35:25 -0400
Subject: [PATCH] Fixed: GSA-392 @arguments with just a short name get the
 wrong argument bindings

-- Now blows up if an argument begins with -.  Implementation isn't pretty, as it actually blows up during Queue extension creation with a somewhat obscure error message but at least its something.
---
 .../sting/commandline/ArgumentDefinition.java   | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
index a5647ec0f..618120217 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.annotation.Annotation;
 import java.util.List;
@@ -147,6 +148,9 @@ public class ArgumentDefinition {
         this.exclusiveOf = exclusiveOf;
         this.validation = validation;
         this.validOptions = validOptions;
+
+        validateName(shortName);
+        validateName(fullName);
     }
 
     /**
@@ -192,6 +196,9 @@ public class ArgumentDefinition {
         else
             shortName = null;
 
+        validateName(shortName);
+        validateName(fullName);
+
         this.ioType = ioType;
         this.argumentType = argumentType;
         this.fullName = fullName;
@@ -277,4 +284,14 @@ public class ArgumentDefinition {
         String validation = (String)CommandLineUtils.getValue(annotation, "validation");
         return validation.trim().length() > 0 ? validation.trim() : null;
     }
+
+    /**
+     * Make sure the argument's name is valid
+     *
+     * @param name
+     */
+    private void validateName(final String name) {
+        if ( name != null && name.startsWith("-") )
+            throw new ReviewedStingException("Invalid argument definition: " + name + " begins with a -");
+    }
 }