From 9207c58b8f9e1f58239e9e3c6d6f6389680a527c Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 17 Jul 2010 22:22:44 +0000
Subject: [PATCH] A fix for the integration test I broke on Friday on my way
 out the door -- some workflows using AlignmentContext were working with it in
 a way I didn't expect and wound up treating extended pileups as base pileups.
  I'll work to make sure the AlignmentContext interface is crystal clear.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3815 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/contexts/AlignmentContext.java               | 6 +++++-
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java   | 4 ++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index c5e2109d8..e2a0be0ce 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
@@ -109,7 +109,11 @@ public class AlignmentContext {
      * extended event (indel) pileup.
      * @return
      */
-    public ReadBackedPileup getBasePileup() { return basePileup; }
+    public ReadBackedPileup getBasePileup() {
+        if(!hasBasePileup())
+            throw new StingException("No base pileup is available.  Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup.");
+        return basePileup;
+    }
 
     /** Returns extended event (indel) pileup over the current genomic location. May return null if this context keeps
      * only base pileup.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 5bbed58c7..c0f2c90ea 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -128,8 +128,8 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
         }
 
         // look at the normal context to get deletions and positions with high entropy
-        ReadBackedPileup pileup = context.getBasePileup();
-        if ( pileup != null ) {
+        if ( context.hasBasePileup() ) {
+            ReadBackedPileup pileup = context.getBasePileup();
 
             int mismatchQualities = 0, totalQualities = 0;
             byte refBase = ref.getBase();