From 88c2fad64f193a42c8e7a66715b27b036a439389 Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Tue, 4 Oct 2011 13:14:39 -0400
Subject: [PATCH] Change vcf jar to use a classfileset to pull all
 dependencies.  Should save Jim Robinson some detective work in the long run.

---
 build.xml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/build.xml b/build.xml
index 1f26e7b7a..34de6cee6 100644
--- a/build.xml
+++ b/build.xml
@@ -545,12 +545,11 @@
 
     <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}">
+	      <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>
         </jar>
     </target>