From 19a4bf9ff06d6b0dc7e70faef6f739553d01b8ff Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Wed, 14 Aug 2013 14:46:17 -0400
Subject: [PATCH] made AR an Advanced argument to discourage basic users from
 fiddling with it

---
 .../broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index 962f81d0d..793877396 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -83,6 +83,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     @Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this IGV formatted file", required = false, defaultToStdout = false)
     public PrintStream activeRegionOutStream = null;
 
+    @Advanced
     @Input(fullName="activeRegionIn", shortName="AR", doc="Use this interval list file as the active regions to process", required = false)
     protected List<IntervalBinding<Feature>> activeRegionBindings = null;