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 1/2] 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"/>

From 26d9c41615ccd502b75f23a42110af925995beba Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 28 Nov 2012 14:06:58 -0500
Subject: [PATCH 2/2] Allow arbitrary resources to be packaged in the GATK jar,
 selecting among public/private/protected appropriately

-Resources must be in a "resources" or "templates" subdirectory within the Java package hierarchy

-Remove direct inclusion of private resources from the main jar packaging target added in Jacob's
patch: this would break builds where the private directory was absent, and did not respect build
settings (include.private, etc.)
---
 build.xml | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/build.xml b/build.xml
index 3a264b476..4db71a9ab 100644
--- a/build.xml
+++ b/build.xml
@@ -226,10 +226,17 @@
     <!-- the path for resources that need to go into the GATK jar;
          any additional resources should go into this set. -->
     <path id="gatk.resources">
-        <fileset dir="${basedir}">
-            <include name="${java.public.source.dir}/**/templates/*" />
-            <include name="${java.private.source.dir}/**/templates/*" if="include.private" />
-            <include name="${java.protected.source.dir}/**/templates/*" if="include.protected" />
+        <fileset dir="${java.public.source.dir}">
+            <include name="**/resources/*" />
+            <include name="**/templates/*" />
+        </fileset>
+        <fileset dir="${java.private.source.dir}" erroronmissingdir="false">
+            <include name="**/resources/*" if="include.private" />
+            <include name="**/templates/*" if="include.private" />
+        </fileset>
+        <fileset dir="${java.protected.source.dir}" erroronmissingdir="false">
+            <include name="**/resources/*" if="include.protected" />
+            <include name="**/templates/*" if="include.protected" />
         </fileset>
     </path>
 
@@ -681,9 +688,6 @@
               <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"/>