From 17ab3a39d55ce389c45f24c81349263e8cd4dad7 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 8 Nov 2012 14:35:23 -0500
Subject: [PATCH] Make the --intermediate_csv_file argument un-hidden.

---
 .../gatk/walkers/bqsr/RecalibrationArgumentCollection.java     | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
index fc7d8a8a4..e5704a1e2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
@@ -75,8 +75,9 @@ public class RecalibrationArgumentCollection {
 
     /**
      * If not provided, then a temporary file is created and then deleted upon completion.
+     * For advanced users only.
      */
-    @Hidden
+    @Advanced
     @Argument(fullName = "intermediate_csv_file", shortName = "intermediate", doc = "The intermediate csv file to create", required = false)
     public File RECAL_CSV_FILE = null;