From da587d48ed6dd78171cd3130215b48ee3dad7d98 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Thu, 27 Feb 2014 04:43:29 +0800
Subject: [PATCH] Using absolute paths in generated diff commands, to ease
 running them from any directory.

---
 .../src/test/java/org/broadinstitute/sting/MD5DB.java           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5DB.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5DB.java
index 7bd6f7bc4..4c0f8b11a 100644
--- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5DB.java
+++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/MD5DB.java
@@ -120,7 +120,7 @@ public class MD5DB {
         for ( String dir : Arrays.asList(GLOBAL_MD5_DB_DIR, LOCAL_MD5_DB_DIR)) {
             File f = getFileForMD5(md5, dir);
             if ( f.exists() && f.canRead() )
-                return f.getPath();
+                return f.getAbsolutePath();
         }
 
         return valueIfNotFound;