From e74c527d47410e7a3a240366783996878ab1f820 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 28 Aug 2012 10:19:18 -0400
Subject: [PATCH] Register the depricated walkers as depricated starting in
 v2.2 so that users get a helpful error message

---
 .../src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index c8dbb090d..00614b9aa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -283,6 +283,8 @@ public class GenomeAnalysisEngine {
     static {
         deprecatedGATKWalkers.put("CountCovariates", "2.0");
         deprecatedGATKWalkers.put("TableRecalibration", "2.0");
+        deprecatedGATKWalkers.put("AlignmentWalker", "2.2");
+        deprecatedGATKWalkers.put("CountBestAlignments", "2.2");
     }
 
     /**