From 43bd4c8e8fdac593ff4a866e47987e017d6b74e6 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 17 Nov 2009 17:20:13 +0000
Subject: [PATCH] Ignoring deletions in the primary pileup by default was
 causing the primary pileup to become shorter than the secondary pileup when
 building up the secondary base pileup string. This fix makes sure to include
 the primary Ds within the pileup so that not only are the pileups guaranteed
 to be the same size, the same offsets will truly correspond with the same
 read.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2058 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/BasicPileup.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/BasicPileup.java b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
index 58b119649..5dcb36df0 100755
--- a/java/src/org/broadinstitute/sting/utils/BasicPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
@@ -190,7 +190,7 @@ abstract public class BasicPileup implements Pileup {
 
         if (sbases == null) { return null; }
 
-        ArrayList<Byte> pbases = basePileup(reads, offsets);
+        ArrayList<Byte> pbases = basePileup(reads, offsets,true);
 
         Random generator = new Random();