From f837e6ced7ac1fc187eb98f3f2c707a18e7f4a8c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 29 Nov 2012 14:38:09 -0500
Subject: [PATCH] Refactored entire NA12878KB to allow us to easily build a
 na12878kb.jar for IGV integration

-- Just separated infrastructure into core package, away from the walkers themselves.
-- Added na12878kb.jar target that builds a jar that can run a test main function (see testNA12878kbJar.csh)
---
 build.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/build.xml b/build.xml
index cc45467d8..834aef3cd 100644
--- a/build.xml
+++ b/build.xml
@@ -679,6 +679,24 @@
         </jar>
     </target>
 
+    <target name="na12878kb.jar" depends="gatk.compile,init.jar">
+        <jar jarfile="${dist.dir}/na12878kb.jar">
+            <fileset dir="${java.classes}">
+              <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
+              <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
+              <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
+              <include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
+              <include name="org/broadinstitute/sting/utils/Utils.class"/>
+              <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
+              <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
+              <include name="net/sf/picard/reference/FastaSequenceFile.class"/>
+            </fileset>
+	    <fileset dir="${java.private.source.dir}">
+              <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
+	    </fileset>
+        </jar>
+    </target>
+
     <target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
         <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
             <path refid="gatk.resources"/>