From c77104b81530e972dd152794551d486fbe622a22 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 6 Apr 2012 00:22:52 -0400
Subject: [PATCH] Adding function call in HaplotypeCaller right before the
 VariantContext gets written out to disk which partitions all the reads by
 which allele gave the read the highest likelihood. This will allow variants
 to be annotated by the refactored VariantAnnotator. Uninformative reads are
 mapped to Allele.NO_CALL

---
 .../org/broadinstitute/sting/utils/Haplotype.java    | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index a8c622a96..03c7d279b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -27,12 +27,11 @@ package org.broadinstitute.sting.utils;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.Cigar;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
@@ -41,6 +40,7 @@ public class Haplotype {
     protected final double[] quals;
     private GenomeLoc genomeLocation = null;
     private HashMap<String, double[]> readLikelihoodsPerSample = null;
+    private HashMap<Integer, VariantContext> eventMap = null;
     private boolean isRef = false;
     private Cigar cigar;
     private int alignmentStartHapwrtRef;
@@ -97,6 +97,14 @@ public class Haplotype {
         return readLikelihoodsPerSample.keySet();
     }
 
+    public HashMap<Integer, VariantContext> getEventMap() {
+        return eventMap;
+    }
+
+    public void setEventMap( final HashMap<Integer, VariantContext> eventMap ) {
+        this.eventMap = eventMap;
+    }
+
     public boolean isReference() {
         return isRef;
     }