From d50f9b98bbad3f37b6ca94e1e8205eb52669aa80 Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Tue, 20 Dec 2011 21:42:30 -0500
Subject: [PATCH] Make sure that the temporary ReadWalker performance
 improvement hack works well in the binary release, jic GATK 1.4 arrives
 before I get a Picard patch.

---
 build.xml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/build.xml b/build.xml
index 232b074f6..04cb243d4 100644
--- a/build.xml
+++ b/build.xml
@@ -847,7 +847,6 @@
 
 
     <path id="testng.default.classpath">
-        <path refid="external.dependencies" />
         <pathelement location="${java.classes}" />
         <pathelement location="${scala.classes}" />
         <pathelement location="${java.contracts}" />
@@ -858,6 +857,7 @@
         <pathelement location="${R.tar.dir}" />
         <pathelement location="${R.public.scripts.dir}" />
         <pathelement location="${R.private.scripts.dir}" />
+        <path refid="external.dependencies" />
     </path>
 
     <path id="testng.gatk.releasetest.classpath">
@@ -1118,6 +1118,11 @@
             <patternset refid="dependency.mask" />
           </fileset>
         </unjar>
+
+        <!-- HACK: The GATK jar itself contains overrides for some core classes.  Make sure the GATK.jar is unrolled last. -->
+        <unjar dest="${staging.dir}" overwrite="true">
+          <fileset dir="${dist.dir}" includes="**/GenomeAnalysisTK.jar"/>
+        </unjar>
     </target>
 
     <!-- Build a package consisting of all supporting files -->