From 8571a641bf5a0c1d35551f7cb0255e65fbdc1d35 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Tue, 3 Dec 2013 16:40:31 -0500
Subject: [PATCH] Add @Advanced to variant_index_type and
 variant_index_parameter

---
 .../sting/gatk/arguments/GATKArgumentCollection.java            | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 1dc760709..08f892f97 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -473,9 +473,11 @@ public class GATKArgumentCollection {
      */
 
     @Argument(fullName="variant_index_type",shortName = "variant_index_type",doc="which type of IndexCreator to use for VCF/BCF indices",required=false)
+    @Advanced
     public GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
 
     @Argument(fullName="variant_index_parameter",shortName = "variant_index_parameter",doc="the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator",required=false)
+    @Advanced
     public int variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
 }