From b732f740d2e0d2bb7a0bf8c2457f630cb0e61782 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 5 Oct 2011 16:51:30 -0400
Subject: [PATCH] Revert "Change vcf jar to use a classfileset to pull all
 dependencies.  Should save"

This reverts commit 441022c4c600624928da46419a6a289200700f3e.
---
 build.xml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/build.xml b/build.xml
index 34de6cee6..1f26e7b7a 100644
--- a/build.xml
+++ b/build.xml
@@ -545,11 +545,12 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-	    <classfileset dir="${java.classes}">
-	      <root classname="org.broadinstitute.sting.utils.variantcontext.VariantContext" />
-	      <root classname="org.broadinstitute.sting.utils.codecs.vcf.VCFCodec" />
-	      <root classname="org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec" />
-	    </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>