Initial commit for Andrey of plumbing for indels. Not finished - need to track down bug with him.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2967 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java

@@ -19,7 +19,8 @@ public abstract class GenotypeCalculationModel implements Cloneable {
 
     public enum Model {
         JOINT_ESTIMATE,
-        POOLED
+        POOLED,
+        INDELS
     }
 
     protected BaseMismatchModel baseModel;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java

@@ -70,6 +70,9 @@ public class GenotypeCalculationModelFactory {
             case POOLED:
                 gcm = new PooledCalculationModel();
                 break;
+            case INDELS:
+                gcm = new SimpleIndelCalculationModel();
+                break;
             default: throw new RuntimeException("Unexpected GenotypeCalculationModel " + UAC.genotypeModel);
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

@@ -0,0 +1,23 @@
+package org.broadinstitute.sting.gatk.walkers.genotyper;
+
+import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.pileup.*;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.contexts.*;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
+
+import java.util.*;
+
+public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
+
+    protected SimpleIndelCalculationModel() {}
+
+    public VariantCallContext callLocus(RefMetaDataTracker tracker, char ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> contexts, DiploidGenotypePriors priors) {
+
+        return null;
+
+        //VariantContext vc = new MutableVariantContext("UG_indel_call", loc, alleles, genotypes, phredScaledConfidence/10.0, null, attributes);
+        //return new VariantCallContext(vc, phredScaledConfidence >= CONFIDENCE_THRESHOLD);
+    }
+}

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -62,9 +62,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     // the calculation arguments
     private UnifiedGenotyperEngine UG_engine = null;
 
-    // Enable deletions in the pileup
+    // enable deletions in the pileup
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
+    // enable extended events for indels
+    public boolean generateExtendedEvents() { return true; }
+    //public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; }
+
     /**
      * Inner class for collecting output statistics from the UG
      */
@@ -170,6 +174,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      * @return the VariantCallContext object
      */
     public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
+        if ( rawContext.hasExtendedEventPileup() )
+            System.out.println("Saw extended event at location " + rawContext.getLocation());
         return UG_engine.runGenotyper(tracker, refContext, rawContext);
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -87,6 +87,9 @@ public class UnifiedGenotyperEngine {
         this.beagleWriter = beagleWriter;
 
         // deal with input errors
+        if ( UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS && !(genotypeWriter instanceof VCFGenotypeWriter) ) {
+            throw new IllegalArgumentException("Attempting to use an output format other than VCF with indels. Please set the output format to VCF.");
+        }
         if ( UAC.POOLSIZE > 0 && UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED ) {
             throw new IllegalArgumentException("Attempting to use a model other than POOLED with pooled data. Please set the model to POOLED.");
         }