From 6f469305ab45db0d7bd7561401789ab4a048625b Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 21 May 2012 10:50:59 -0400
Subject: [PATCH] Don't try to share BCF2 yet

---
 build.xml                                                      | 2 +-
 .../sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/build.xml b/build.xml
index c72ec9bac..3775780f1 100644
--- a/build.xml
+++ b/build.xml
@@ -641,7 +641,7 @@
         <jar jarfile="${dist.dir}/vcf.jar">
             <fileset dir="${java.classes}">
               <include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
-              <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
+<!--               <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/> -->
               <include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
               <include name="org/broadinstitute/sting/utils/exceptions/**"/>
 	          <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
index 4416e02ab..fa5476150 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
@@ -50,7 +50,8 @@ public class VCFJarClassLoadingUnitTest {
 
         ClassLoader classLoader = new URLClassLoader(jarURLs, null);
         classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
-        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
+// TODO -- uncomment when we include BCF2 codec
+//        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
         classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
         classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
         classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter");