From 921f551426f47df7b837b95ed76bfda59c15c9f5 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 8 Jul 2013 09:48:12 -0400
Subject: [PATCH] AnalyzeCovariates is no longer a deprecated tool.

---
 .../src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java b/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
index e20872c5b..78c32ed02 100644
--- a/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
+++ b/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
@@ -43,7 +43,6 @@ public class DeprecatedToolChecks {
     static {
         // Indicate recommended replacement in parentheses if applicable
         deprecatedGATKWalkers.put("CountCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
-        deprecatedGATKWalkers.put("AnalyzeCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
         deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
         deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
         deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");