From dd780dba5fa5b07591bda94b58ac505e9131ca89 Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Wed, 5 Oct 2011 18:25:26 -0400
Subject: [PATCH] Rather than just picking a few classes to be the roots of the
 vcf jar and including all dependencies, use the entire codecs.vcf and
 variantcontext packages as roots.

Fix for my fix for Jim Robinson.
---
 build.xml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/build.xml b/build.xml
index 1f26e7b7a..1e5aaf644 100644
--- a/build.xml
+++ b/build.xml
@@ -545,12 +545,10 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-            <fileset dir="${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>
+	    <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>
         </jar>
     </target>