From 1af76736b9dc41da345df90648ec5d74ade03f70 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sun, 17 Jul 2011 11:41:34 -0400
Subject: [PATCH] Guarantees that the list of files will always be in the same
 order.

---
 .../src/org/broadinstitute/sting/queue/util/QScriptUtils.scala  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
index 9fb4fa30d..99aaa9474 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -31,7 +31,7 @@ object QScriptUtils {
     for (bam <- fromFile(in).getLines)
       if (!bam.startsWith("#") && !bam.isEmpty )
         list :+= new File(bam.trim())
-    list
+    list.sortWith(_.compareTo(_) < 0)
   }
 
   /**