From 1975de1b3220f9827e938b010141f7d32a72de7b Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Tue, 11 Oct 2011 11:11:29 -0400
Subject: [PATCH] Second try: hide --do_indel_quality in AnalyzeCovariates

---
 .../sting/analyzecovariates/AnalyzeCovariates.java               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
index 1ef452a5c..548678ddb 100755
--- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
@@ -135,6 +135,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
      */
     @Argument(fullName="max_histogram_value", shortName="maxHist", required = false, doc="If supplied, this value will be the max value of the histogram plots")
     private int MAX_HISTOGRAM_VALUE = 0;
+    @Hidden
     @Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting")
     private boolean DO_INDEL_QUALITY = false;