From 488622041d09ad73c8f83b559f21a0a750b49c13 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 Apr 2011 18:00:48 +0000
Subject: [PATCH] Further trivial cleanup: Renamed
 DindelGenotypeLikelihoodsCalculationModel to
 IndelGenotypeLikelihoodsCalculationModel

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5616 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...del.java => IndelGenotypeLikelihoodsCalculationModel.java} | 4 ++--
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename java/src/org/broadinstitute/sting/gatk/walkers/genotyper/{DindelGenotypeLikelihoodsCalculationModel.java => IndelGenotypeLikelihoodsCalculationModel.java} (98%)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index e37b0ccc5..e5a9927e4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -47,7 +47,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
 
-public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
+public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
     private final int maxReadDeletionLength = 3;
     private final int HAPLOTYPE_SIZE;
 
@@ -66,7 +66,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
     private GenomeLoc lastSiteVisited;
     private List<Allele> alleleList;
 
-    protected DindelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
+    protected IndelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
             pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY,UAC.INDEL_GAP_CONTINUATION_PENALTY,
                     UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.DO_CONTEXT_DEPENDENT_PENALTIES, UAC.dovit);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index c0d092afd..db860029b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -638,7 +638,7 @@ public class UnifiedGenotyperEngine {
     private static Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) {
         Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel>();
         glcm.put(GenotypeLikelihoodsCalculationModel.Model.SNP, new SNPGenotypeLikelihoodsCalculationModel(UAC, logger));
-        glcm.put(GenotypeLikelihoodsCalculationModel.Model.INDEL, new DindelGenotypeLikelihoodsCalculationModel(UAC, logger));
+        glcm.put(GenotypeLikelihoodsCalculationModel.Model.INDEL, new IndelGenotypeLikelihoodsCalculationModel(UAC, logger));
         return glcm;
     }