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] 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"/>