Fixes for getting ValidatingPileup running in parallel.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
+import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
@@ -42,8 +43,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
      */
     private static final int MAX_OUTSTANDING_OUTPUT_MERGES = 50;
 
-    private TraverseLoci traversalEngine = null;
-
     /**
      * Manage currently running threads.
      */
@@ -62,8 +61,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
     protected HierarchicalMicroScheduler( Walker walker, Reads reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse ) {
         super( walker, reads, refFile, rods );
         this.threadPool = Executors.newFixedThreadPool(nThreadsToUse);
-        if( !(traversalEngine instanceof TraverseLoci) )
-            throw new UnsupportedOperationException("Traversal engine supports only traverse loci by reference at this time.");
     }
 
     public Object execute( Walker walker, List<GenomeLoc> intervals ) {
@@ -211,7 +208,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
         Shard shard = traverseTasks.remove();
         OutputMerger outputMerger = new OutputMerger();
 
-        ShardTraverser traverser = new ShardTraverser( traversalEngine,
+        ShardTraverser traverser = new ShardTraverser( getTraversalEngine(),
                                                        walker,
                                                        shard,
                                                        getShardDataProvider(shard),

java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
-import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
+import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.OutputTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -25,12 +25,12 @@ import java.util.concurrent.Callable;
  */
 public class ShardTraverser implements Callable {
     private Walker walker;
-    private TraverseLoci traversalEngine;
+    private TraversalEngine traversalEngine;
     private Shard shard;
     private ShardDataProvider dataProvider;
     private OutputMerger output;
 
-    public ShardTraverser( TraverseLoci traversalEngine,
+    public ShardTraverser( TraversalEngine traversalEngine,
                            Walker walker,
                            Shard shard,
                            ShardDataProvider dataProvider,

java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java

@@ -8,6 +8,7 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.Pileup;
 import org.broadinstitute.sting.utils.BasicPileup;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Created by IntelliJ IDEA.
@@ -17,7 +18,7 @@ import org.broadinstitute.sting.utils.ReadBackedPileup;
  * To change this template use File | Settings | File Templates.
  */
 @Requires(value={DataSource.READS,DataSource.REFERENCE},referenceMetaData=@RMD(name="pileup",type=rodSAMPileup.class))
-public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats> {
+public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats>  implements TreeReducible<ValidationStats> {
     @Argument(fullName="continue_after_error",doc="Continue after an error",required=false)
     public boolean CONTINUE_AFTER_AN_ERROR = false;
 
@@ -51,6 +52,13 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         sum.nBases += value;
         return sum;
     }
+
+    public ValidationStats treeReduce( ValidationStats lhs, ValidationStats rhs ) {
+        ValidationStats combined = new ValidationStats();
+        combined.nLoci = lhs.nLoci + rhs.nLoci;
+        combined.nBases = lhs.nBases + rhs.nBases;
+        return combined;
+    }
 }
 
 class ValidationStats {