From 2ef2f1b24ad2b64604a02a3c6cf8d9c4886c08af Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Aug 2010 15:35:47 +0000
Subject: [PATCH] Fix UG's simple indel calculation model so that deletions are
 created correctly

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4072 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/genotyper/SimpleIndelCalculationModel.java    | 3 ++-
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java         | 1 -
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
index b4ad9b7c4..7750ebdf1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
@@ -69,7 +69,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
             if ( bestEvent.charAt(0) == '-' ) {
                 alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,false) );
                 alleles.add( Allele.create(bestEvent.substring(1), true ));
-                loc = GenomeLocParser.setStop(loc, loc.getStop() + bestEvent.length()-2);
+                loc = GenomeLocParser.setStop(loc, loc.getStop() + bestEvent.length()-1);
             } else
                 throw new StingException("Internal error (probably a bug): event does not conform to expected format: "+ bestEvent);
         }
@@ -78,6 +78,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
                 -1.0 /* log error */, null /* filters */, null /* attributes */);
 
         vcc = new VariantCallContext(vc,true);
+        vcc.setRefBase(ref[0]);
 /*
         if ( totalIndels > 0 ) {
             System.out.println("Calling: "+bestEvent+" ["+bestIndelCount+"/"+totalIndels+"/"+totalCoverage+"] at "+loc);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 15a763bfc..7c9e74939 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.util.*;