From 46362ce5321caf39ef06632f6070c2e26469dcbb Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 30 Dec 2009 21:57:20 +0000
Subject: [PATCH] In extended event lines, now prints deletions in verbose
 format as well (e.g. "-AAT")

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2490 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/walkers/PileupWalker.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index b9f664251..07707525a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -91,7 +91,8 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
 
         if ( context.hasExtendedEventPileup() ) {
             ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
-            List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts();
+            List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts(ref.getBases());
+
             out.printf("%s %s ", indelPileup.getShortPileupString(), rods);
             int i = 0;
             for ( ; i < eventCounts.size() - 1 ; i++ ) {