From b4baa3eb8fccbf719bb1832ec28b74a304876e17 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Aug 2010 14:52:51 +0000
Subject: [PATCH] Cleanup.  INDELS model is now disconnected (and renamed
 'DINDEL' in preparation for adding plumbing for Guillermo soon)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4106 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/genotyper/BatchedCallsMerger.java  |  2 +-
 .../genotyper/DiploidGenotypeCalculationModel.java  |  8 +-------
 .../walkers/genotyper/GenotypeCalculationModel.java |  3 +--
 .../genotyper/GenotypeCalculationModelFactory.java  | 13 ++++++-------
 .../gatk/walkers/genotyper/UnifiedGenotyper.java    |  4 +---
 .../walkers/genotyper/UnifiedGenotyperEngine.java   |  2 +-
 6 files changed, 11 insertions(+), 21 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
index 0c22bb6f3..17db761eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
@@ -71,7 +71,7 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
     // enable extended events for indels
-    public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; }
+    public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.DINDEL; }
 
     public void initialize() {
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
index f0e4b1683..571cdff55 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@@ -37,14 +37,8 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import java.util.*;
 
 public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalculationModel {
-    /**
-     * Should we enable the experimental genotype likelihood calculations?
-     */
-    protected boolean useExptGenotypeLikelihoods = false;
 
-    protected DiploidGenotypeCalculationModel(boolean useExptGenotypeLikelihoods) {
-        this.useExptGenotypeLikelihoods = useExptGenotypeLikelihoods;
-    }
+    protected DiploidGenotypeCalculationModel() {}
 
     // the GenotypeLikelihoods map
     private HashMap<String, GenotypeLikelihoods> GLs = new HashMap<String, GenotypeLikelihoods>();
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 c3208031a..65b194c45 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
@@ -21,8 +21,7 @@ public abstract class GenotypeCalculationModel implements Cloneable {
 
     public enum Model {
         JOINT_ESTIMATE,
-        JOINT_ESTIMATE_EXPT_GL,
-        INDELS
+        DINDEL
     }
 
     protected UnifiedArgumentCollection UAC;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
index 238b0bcb3..79fef9aac 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
@@ -55,14 +55,13 @@ public class GenotypeCalculationModelFactory {
         GenotypeCalculationModel gcm;
         switch ( UAC.genotypeModel ) {
             case JOINT_ESTIMATE:
-            case JOINT_ESTIMATE_EXPT_GL:
-                boolean useExptGenotypeLikelihoods = UAC.genotypeModel == JOINT_ESTIMATE_EXPT_GL;
-                gcm = new DiploidGenotypeCalculationModel(useExptGenotypeLikelihoods);
+                gcm = new DiploidGenotypeCalculationModel();
                 break;
-            case INDELS:
-                gcm = new SimpleIndelCalculationModel();
-                break;
-            default: throw new RuntimeException("Unexpected GenotypeCalculationModel " + UAC.genotypeModel);
+            case DINDEL:
+                throw new UnsupportedOperationException("The Dindel-based genotype likelihoods model is not currently supported");
+                //gcm = new SimpleIndelCalculationModel();
+                //break;
+            default: throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + UAC.genotypeModel);
         }
 
         gcm.initialize(samples, logger, UAC, verboseWriter);
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 fb7c72fa2..2663a8999 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -37,8 +37,6 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.util.*;
 import java.io.PrintStream;
-import java.io.File;
-import java.io.FileNotFoundException;
 
 
 /**
@@ -85,7 +83,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
     // enable extended events for indels
-    public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; }
+    public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.DINDEL; }
 
     /**
      * Inner class for collecting output statistics from the UG
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 cfb4a32cf..75c3f23d2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -175,7 +175,7 @@ public class UnifiedGenotyperEngine {
                 return null;
 
             // are there too many deletions in the pileup?
-            if ( UAC.genotypeModel != GenotypeCalculationModel.Model.INDELS &&
+            if ( UAC.genotypeModel != GenotypeCalculationModel.Model.DINDEL &&
                  isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) &&
                  (double)pileup.getNumberOfDeletions() / (double)pileup.size() > UAC.MAX_DELETION_FRACTION )
                 return null;