From c7e357eb599b1c50e75fb610dd415f89af1cbd19 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Fri, 11 Jul 2014 23:19:42 +0800
Subject: [PATCH] Added cofoja to the gatk packages for tests to pass.

---
 protected/gatk-package-distribution/pom.xml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/protected/gatk-package-distribution/pom.xml b/protected/gatk-package-distribution/pom.xml
index 39ac52e58..3896affeb 100644
--- a/protected/gatk-package-distribution/pom.xml
+++ b/protected/gatk-package-distribution/pom.xml
@@ -58,6 +58,18 @@
             <groupId>commons-httpclient</groupId>
             <artifactId>commons-httpclient</artifactId>
         </dependency>
+        <!--
+        Some cofoja annotations (ex: PreconditionError) are ONLY in used tests.
+        They are not picked up by shade, not required during normal runs, but are important for tests to avoid
+        the cryptic ArrayStoreExceptions. See also: http://bugs.java.com/view_bug.do?bug_id=7183985
+        If added as scope test, they are not included during runtime compilation.
+        So, as a workaround, could configure shade to just include the classes, but our
+        standard operating procedure so far has been to include classes as full artifacts.
+        -->
+        <dependency>
+            <groupId>com.google.code.cofoja</groupId>
+            <artifactId>cofoja</artifactId>
+        </dependency>
         <!-- Required for binary-dist assembly, excluded by shade -->
         <dependency>
             <groupId>${project.groupId}</groupId>