From bc842ab3a5d60095aadff6bae4d271615d0ea294 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sun, 18 Dec 2011 15:27:23 -0500
Subject: [PATCH] Adding option to VariantAnnotator to do strict allele
 matching when annotating with comp track concordance.

---
 .../gatk/walkers/annotator/VariantAnnotator.java   |  4 ++++
 .../walkers/annotator/VariantAnnotatorEngine.java  | 14 ++++++++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 4fa6d0bbf..69560c7cb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -170,6 +170,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio")
     public double minGenotypeQualityP = 0.0;
 
+    @Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp tracks that exactly match both reference and alternate alleles will be counted as concordant", required=false)
+    private boolean requireStrictAlleleMatch = false;
+
     private VariantAnnotatorEngine engine;
 
     private Collection<VariantContext> indelBufferContext;
@@ -211,6 +214,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         else
             engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
         engine.initializeExpressions(expressionsToUse);
+        engine.setRequireStrictAlleleMatch(requireStrictAlleleMatch);
 
         // setup the header fields
         // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index d4442dc5d..98d2fe17b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -47,9 +47,11 @@ public class VariantAnnotatorEngine {
     private List<GenotypeAnnotation> requestedGenotypeAnnotations;
     private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
 
-    private HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>();
-    private AnnotatorCompatibleWalker walker;
-    private GenomeAnalysisEngine toolkit;
+    private final HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>();
+    private final AnnotatorCompatibleWalker walker;
+    private final GenomeAnalysisEngine toolkit;
+
+    private boolean requireStrictAlleleMatch = false;
 
     protected static class VAExpression {
 
@@ -163,6 +165,10 @@ public class VariantAnnotatorEngine {
         return descriptions;
     }
 
+    public void setRequireStrictAlleleMatch( final boolean requireStrictAlleleMatch ) {
+        this.requireStrictAlleleMatch = requireStrictAlleleMatch;
+    }
+
     public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes());
 
@@ -197,7 +203,7 @@ public class VariantAnnotatorEngine {
             } else {
                 boolean overlapsComp = false;
                 for ( VariantContext comp : tracker.getValues(dbSet.getKey(), ref.getLocus()) ) {
-                    if ( !comp.isFiltered() ) {
+                    if ( !comp.isFiltered() && ( !requireStrictAlleleMatch || comp.getAlleles().equals(vc.getAlleles()) ) ) {
                         overlapsComp = true;
                         break;
                     }