From efca1fdfd8a5e6cf25062911f142bb1bfcabea9b Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Thu, 6 Oct 2011 10:08:48 -0400
Subject: [PATCH] Revert change until I figure out how to use
 classfileset/rootfileset with a vanilla ant install.

This reverts commit 4c9022872beec8dc0700a1320a267e3603c8212d.
---
 build.xml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/build.xml b/build.xml
index 1e5aaf644..1f26e7b7a 100644
--- a/build.xml
+++ b/build.xml
@@ -545,10 +545,12 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-	    <classfileset dir="${java.classes}">
-	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/codecs/vcf/**/*.class" />
-	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/variantcontext/**/*.class" />
-	    </classfileset>
+            <fileset dir="${java.classes}">
+              <include name="**/utils/codecs/**/*.class"/>
+              <include name="**/utils/variantcontext/**/*.class"/>
+              <include name="org/broadinstitute/sting/utils/exceptions/**"/>
+	      <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
+            </fileset>
         </jar>
     </target>