From 438a7ad0985a789203b43f8771731b02ee7168ba Mon Sep 17 00:00:00 2001
From: Steve Huang <shuang@broadinstitute.org>
Date: Wed, 31 Jul 2019 12:54:24 -0400
Subject: [PATCH] a bug fix suggested by Louis

---
 .../engine/spark/datasources/ReferenceFileSparkSource.java      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReferenceFileSparkSource.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReferenceFileSparkSource.java
index f165c9c8b5a..fc0fdc40ccb 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReferenceFileSparkSource.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReferenceFileSparkSource.java
@@ -50,7 +50,7 @@ public ReferenceFileSparkSource( final Path referencePath) {
 
     private synchronized Path getReferencePath() {
         if (null == referencePath) {
-            this.referencePath = Paths.get(referenceUri);
+            this.referencePath = IOUtils.getPath(referenceUri.toString());
         }
         return referencePath;
     }