From 5aa79dacfc63895ab7ab96d1b17ea43b35230f37 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 16 Dec 2011 10:29:20 -0500
Subject: [PATCH] Changing hidden optimization argument to advanced.

---
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 339b8e0e6..7cc5b1625 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -175,7 +175,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     /////////////////////////////
     // Debug Arguments
     /////////////////////////////
-    @Hidden
+    @Advanced
     @Argument(fullName = "trustAllPolymorphic", shortName = "allPoly", doc = "Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation.", required = false)
     protected Boolean TRUST_ALL_POLYMORPHIC = false;
     //@Hidden