From 4bdb5b03bd20ddea6088ec5567622b83608962b2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 30 Oct 2009 03:10:44 +0000
Subject: [PATCH] tell UnifiedGenotyper to return calls at all bases

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index f10a90a04..f3fd3e456 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -64,6 +64,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
         ug.initialize();
         uac.baseModel = BaseMismatchModel.THREE_STATE;
+        uac.ALL_BASES = true;
         ug.setUnifiedArgumentCollection(uac);
         // refWindow = new ReferenceContextWindow(nPreviousBases);
         usePreviousBases = new ArrayList<Boolean>();