From 03bf75e335e9dbcd48bf86eaa034091f10662216 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 22 Dec 2009 17:52:51 +0000
Subject: [PATCH] Now implements TreeReducible

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2427 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/genotyper/UnifiedGenotyper.java  | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

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 cb71a95af..232d67dcb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -48,7 +48,7 @@ import java.util.*;
  */
 @Reference(window=@Window(start=-20,stop=20))
 @ReadFilters({ZeroMappingQualityReadFilter.class,MappingQualityReadFilter.class,BadMateReadFilter.class})
-public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genotype>>, Integer> {
+public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genotype>>, Integer> implements TreeReducible<Integer> {
 
     @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
 
@@ -62,8 +62,6 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
     // samples in input
     private Set<String> samples;
 
-    // keep track of some metrics about our calls
-    private CallMetrics callsMetrics;
 
     /** Enable deletions in the pileup **/
     public boolean includeReadsWithDeletionAtLoci() { return true; }
@@ -144,8 +142,6 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
 
         // initialize the header
         GenotypeWriterFactory.writeHeader(writer, GenomeAnalysisEngine.instance.getSAMFileHeader(), samples, headerInfo);
-
-        callsMetrics = new CallMetrics();
     }
 
     private Set<VCFHeaderLine> getHeaderInfo() {
@@ -254,22 +250,21 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
 
     public Integer reduceInit() { return 0; }
 
+    public Integer treeReduce(Integer lhs, Integer rhs) {
+        return lhs + rhs;        
+    }
+
     public Integer reduce(Pair<VariationCall, List<Genotype>> value, Integer sum) {
         // can't call the locus because of no coverage
         if ( value == null )
             return sum;
 
-        callsMetrics.nCalledBases++;
-
         // can't make a confident variant call here
         if ( value.second == null ||
                 (UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED && value.second.size() == 0) ) {
-            callsMetrics.nNonConfidentCalls++;
             return sum;
         }
 
-        callsMetrics.nConfidentCalls++;
-
         // if we have a single-sample call (single sample from PointEstimate model returns no VariationCall data)
         if ( value.first == null || (!writer.supportsMultiSample() && samples.size() <= 1) ) {
             writer.addGenotypeCall(value.second.get(0));