From c313abf0bea4a10eedde4ac7c46fc5c760bb6ffa Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 Nov 2009 00:15:45 +0000
Subject: [PATCH] Restore a jar packaging change that got clobbered.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1962 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/build.xml b/build.xml
index 05389ad68..d15a93cf1 100644
--- a/build.xml
+++ b/build.xml
@@ -101,7 +101,10 @@
         </jar>
 
         <jar jarfile="${dist}/GenomeAnalysisTK.jar">
-            <fileset dir="build" includes="**/gatk/**/*.class"/>
+            <fileset dir="build">
+              <include name="**/gatk/**/*.class" />
+              <include name="**/alignment/**/*.class"/>
+            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK"/>
             </manifest>