From f096a958d6a1ac989bbe81c1b0ac6c83049d83f1 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 9 Mar 2010 19:13:01 +0000
Subject: [PATCH] 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
---
 .../genotyper/GenotypeCalculationModel.java   |  3 ++-
 .../GenotypeCalculationModelFactory.java      |  3 +++
 .../SimpleIndelCalculationModel.java          | 23 +++++++++++++++++++
 .../walkers/genotyper/UnifiedGenotyper.java   |  8 ++++++-
 .../genotyper/UnifiedGenotyperEngine.java     |  3 +++
 5 files changed, 38 insertions(+), 2 deletions(-)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

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 30d2d1c3c..e13bab43c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
+++ b/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;
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 e97af33ad..a3d258d82 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
+++ b/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);
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
new file mode 100755
index 000000000..bd76cd10f
--- /dev/null
+++ b/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);
+    }
+}
\ No newline at end of file
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 b02b1649a..6ec9ed068 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/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);
     }
 
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 552a006e7..7c6a43270 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/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.");
         }