From 5d2fab93f4aa36d681acbe4217c7c1d29394dbdc Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Apr 2010 17:40:30 +0000
Subject: [PATCH] Method signature changed: for extended events, pass array of
 reference bases (to ensure we cover the full length of the indel event), not
 just reference base.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/GenotypeCalculationModel.java  | 2 +-
 .../genotyper/JointEstimateGenotypeCalculationModel.java        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
index 8f61de56c..7e1027823 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
@@ -102,7 +102,7 @@ public abstract class GenotypeCalculationModel implements Cloneable {
      * @return call
      */
     public abstract VariantCallContext callExtendedLocus(RefMetaDataTracker tracker,
-                                                         char ref,
+                                                         char[] ref,
                                                          GenomeLoc loc,
                                                          Map<String, StratifiedAlignmentContext> stratifiedContexts);
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index 1701e2b37..f8ca92d73 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -40,7 +40,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
 
     protected JointEstimateGenotypeCalculationModel() {}
 
-    public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> stratifiedContexts) {
+    public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char[] ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> stratifiedContexts) {
         return null;
     }