From 1cc0b48caab07426a3d54b34db3043ca96a28a4e Mon Sep 17 00:00:00 2001
From: Jacob Silterra <jacob@broadinstitute.org>
Date: Tue, 27 Nov 2012 17:44:35 -0500
Subject: [PATCH] Abstract connection to MongoDB so we can specify it through
 JSON file. Include 2 JSON spec files in GenomeAnalysisTK.jar

Create MongoDBManager, which keeps track of connections based on Locator class. Locators can be instantiated directly, or read from JSON files (NA12878DBArgumentCollection uses the GSon library)
---
 build.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/build.xml b/build.xml
index a93918ec8..3a264b476 100644
--- a/build.xml
+++ b/build.xml
@@ -681,6 +681,9 @@
               <include name="**/gatk/**/*.class" />
               <include name="**/alignment/**/*.class"/>
             </fileset>
+            <fileset dir="${java.private.source.dir}">
+                <include name="**/gatk/**/resources/*.*" />
+            </fileset>
             <fileset dir="${R.script.staging.dir}">
                 <include name="**/gatk/**/*.R"/>
                 <include name="**/alignment/**/*.R"/>