From aec83b401d5192dd5c647fd5038d7965d884b8c0 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 5 Oct 2009 19:48:57 +0000
Subject: [PATCH] SSG multithreading doesn't play well with some I/O changes
 made since I last svn up'd.  Reverting until I can find the reason.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1766 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/SingleSampleGenotyper.java      | 44 ++++++-------------
 1 file changed, 13 insertions(+), 31 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java
index 937d48840..dbd58589a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java
@@ -7,7 +7,6 @@ import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
@@ -17,7 +16,7 @@ import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
 import java.io.File;
 
 @ReadFilters(ZeroMappingQualityReadFilter.class)
-public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSampleGenotyper.CallResult> implements TreeReducible<SingleSampleGenotyper.CallResult> {
+public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSampleGenotyper.CallResult> {
     // Control output settings
     @Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = false)
     public File VARIANTS_FILE = null;
@@ -48,16 +47,17 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
     @Argument(fullName = "disableCache", doc = "[ADVANCED] If true, we won't use the caching system.  This argument is for testing purposes only", required = false)
     public boolean disableCache = false;
 
-    /**
-     * Writer for genotype data.
-     */
-    private GenotypeWriter genotypeWriter;
 
     public class CallResult {
         long nConfidentCalls = 0;
         long nNonConfidentCalls = 0;
         long nCalledBases = 0;
+        GenotypeWriter writer;
 
+        CallResult(GenotypeWriter writer) {
+            this.writer = writer;
+        }
+        
         public String toString() {
             return String.format("SSG: %d confident and %d non-confident calls were made at %d bases", 
                     nConfidentCalls, nNonConfidentCalls, nCalledBases);
@@ -80,10 +80,7 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
     /** Initialize the walker with some sensible defaults */
     public void initialize() {
         //GenotypeLikelihoods.clearCache();
-        if ( VARIANTS_FILE != null )
-            genotypeWriter = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE);
-        else
-            genotypeWriter = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out);
+        // nothing to do
     }
 
     /**
@@ -141,7 +138,10 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
      * @return an empty string
      */
     public CallResult reduceInit() {
-        return new CallResult();
+        if ( VARIANTS_FILE != null )
+            return new CallResult(GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE));
+        else
+            return new CallResult(GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out));
     }
 
     /**
@@ -160,34 +160,16 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
             if (confidence >= LOD_THRESHOLD) {
                 sum.nConfidentCalls++;
                 //System.out.printf("Call %s%n", call);
-                genotypeWriter.addGenotypeCall(call);
+                sum.writer.addGenotypeCall(call);
             } else
                 sum.nNonConfidentCalls++;
         }
         return sum;
     }
 
-    /**
-     * Combine adjacent call results.
-     *
-     * @param lhs first set of partial call results from genotyper; guaranteed to have come from 'earlier' in genome.
-     * @param rhs second set of partial call results from genotyper; guaranteed to have come from 'later' in genome.
-     *
-     * @return combined call results.
-     */
-    public CallResult treeReduce( CallResult lhs, CallResult rhs ) {
-        CallResult combined = new CallResult();
-        combined.nCalledBases = lhs.nCalledBases + rhs.nCalledBases;
-        combined.nConfidentCalls = lhs.nConfidentCalls + rhs.nConfidentCalls;
-        combined.nNonConfidentCalls = lhs.nNonConfidentCalls + rhs.nNonConfidentCalls;
-        return combined;
-    }
-
     /** Close the variant file. */
     public void onTraversalDone(CallResult sum) {
-        // If the VARIANTS_FILE is null, the GATK is managing the output stream.  Close the file.
-        if ( VARIANTS_FILE == null )
-            genotypeWriter.close();        
+        sum.writer.close();
     }
 }