From 533c283783a9b9e2e6c1e511ce0825f52df46a1f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 30 Mar 2012 10:37:14 -0400
Subject: [PATCH] Deprecating AlignmentContext.getExtendedEventPileup().  At
 this point the only walkers left with any relaiance on extended events are
 Guillermo's pooled code (he'll update soon) and the Pileup walker.  David,
 I'll leave that last one for you (it should be easy).  We can now officially
 rip the extended event code from the engine.

---
 .../broadinstitute/sting/gatk/contexts/AlignmentContext.java    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index 57416d111..9a847d38e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
@@ -98,6 +98,7 @@ public class AlignmentContext implements HasGenomeLocation {
      * only base pileup.
      * @return
      */
+    @Deprecated
     public ReadBackedExtendedEventPileup getExtendedEventPileup() {
         if(!hasExtendedEventPileup())
             throw new ReviewedStingException("No extended event pileup is present.");
@@ -115,6 +116,7 @@ public class AlignmentContext implements HasGenomeLocation {
      *
      * @return
      */
+    @Deprecated
     public boolean hasExtendedEventPileup() { return basePileup instanceof ReadBackedExtendedEventPileup; }
 
     /**