From c6ef6ee8b7859890f96fbf8214a9ad91c26c9334 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Mar 2011 12:08:58 +0000
Subject: [PATCH] Recal file is in input to ApplyRecalibration not an output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5452 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/ApplyRecalibration.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 53c480b96..77ef59ca0 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -60,7 +60,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
     /////////////////////////////
     // Inputs
     /////////////////////////////
-    @Output(fullName="recal_file", shortName="recalFile", doc="The output recal file used by ApplyRecalibration", required=true)
+    @Input(fullName="recal_file", shortName="recalFile", doc="The output recal file used by ApplyRecalibration", required=true)
     private File RECAL_FILE;
     @Input(fullName="tranches_file", shortName="tranchesFile", doc="The input tranches file describing where to cut the data", required=true)
     private File TRANCHES_FILE;