From 7bbd67f3c47b55288981fbb8c21e1ea076b1caf0 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Aug 2010 20:19:39 +0000
Subject: [PATCH] Fixing stray comments.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4102 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../GenerateVariantClustersWalker.java                 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 575e9a20c..35dc5bc0d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -78,11 +78,11 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
     private int MAX_GAUSSIANS = 4;
     @Argument(fullName="maxIterations", shortName="mI", doc="The maximum number of iterations to be performed when clustering. Clustering will normally end when convergence is detected.", required=false)
     private int MAX_ITERATIONS = 200;
-    @Argument(fullName = "path_to_Rscript", shortName="Rscript", doc="The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
- //   private String PATH_TO_RSCRIPT = "Rscript";
- //   @Argument(fullName = "path_to_resources", shortName = "resources", doc="Path to resources folder holding the Sting R scripts.", required=false)
- //   private String PATH_TO_RESOURCES = "R/";
- //   @Argument(fullName="weightNovels", shortName="weightNovels", doc="The weight for novel variants during clustering", required=false)
+//    @Argument(fullName = "path_to_Rscript", shortName="Rscript", doc="The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
+//    private String PATH_TO_RSCRIPT = "Rscript";
+//    @Argument(fullName = "path_to_resources", shortName = "resources", doc="Path to resources folder holding the Sting R scripts.", required=false)
+//    private String PATH_TO_RESOURCES = "R/";
+    @Argument(fullName="weightNovels", shortName="weightNovels", doc="The weight for novel variants during clustering", required=false)
     private double WEIGHT_NOVELS = 0.0;
     @Argument(fullName="weightKnowns", shortName="weightKnowns", doc="The weight for MQ2+ known variants during clustering", required=false)
     private double WEIGHT_KNOWNS = 0.0;