From 1ce0b9d519a1bc3c323a660071598ffafea0ee57 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Thu, 28 Jun 2012 11:21:11 -0400
Subject: [PATCH] Throwing UnknownTribbleType exception instead of
 CommandLineException when an unknown tribble type is specified.

---
 .../sting/commandline/ArgumentTypeDescriptor.java              | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index d5503b2a9..c201e95f0 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -345,7 +345,8 @@ public abstract class ArgumentTypeDescriptor {
 
                 FeatureManager manager = new FeatureManager();
                 if ( manager.getByName(tribbleType) == null )
-                    throw new UserException.CommandLineException(
+                    throw new UserException.UnknownTribbleType(
+                            tribbleType,
                             String.format("Unable to find tribble type '%s' provided on the command line. " +
                                     "Please select a correct type from among the supported types:%n%s",
                                     tribbleType, manager.userFriendlyListOfAvailableFeatures(parameterType)));