Optimizations for parallel read walkers

-- TraversalReadsNano only creates the NanoScheduler once, and shuts it down onTraversalDone
-- Nicer debugging output in NanoScheduler
-- ReadShard has a getBufferSize() method now

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java

@@ -58,6 +58,15 @@ public class ReadShard extends Shard {
         MAX_READS = bufferSize;
     }
 
+    /**
+     * What read buffer size are we using?
+     *
+     * @return
+     */
+    public static int getReadBufferSize() {
+        return MAX_READS;
+    }
+
     /**
      * Returns true if this shard is meant to buffer reads, rather
      * than just holding pointers to their locations.

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java

@@ -51,12 +51,12 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
     /** our log, which we want to capture anything from this class */
     protected static final Logger logger = Logger.getLogger(TraverseReadsNano.class);
     private static final boolean DEBUG = false;
-    final int bufferSize = ReadShard.MAX_READS;
-    final int mapGroupSize = bufferSize / 10 + 1;
-    final int nThreads;
+    final NanoScheduler<SAMRecord, M, T> nanoScheduler;
 
     public TraverseReadsNano(int nThreads) {
-        this.nThreads = nThreads;
+        final int bufferSize = ReadShard.getReadBufferSize() + 1; // actually has 1 more than max
+        final int mapGroupSize = bufferSize / 10 + 1;
+        nanoScheduler = new NanoScheduler<SAMRecord, M, T>(bufferSize, mapGroupSize, nThreads);
     }
 
     @Override
@@ -87,18 +87,23 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
         final ReadReferenceView reference = new NotImplementedReadReferenceView(dataProvider);
         final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
 
-        final NanoScheduler<SAMRecord, M, T> nanoScheduler = new NanoScheduler<SAMRecord, M, T>(bufferSize, mapGroupSize, nThreads);
         nanoScheduler.setDebug(DEBUG);
         final TraverseReadsMap myMap = new TraverseReadsMap(reads, reference, rodView, walker);
         final TraverseReadsReduce myReduce = new TraverseReadsReduce(walker);
 
         T result = nanoScheduler.execute(reads.iterator().iterator(), myMap, sum, myReduce);
-        nanoScheduler.shutdown();
+        // TODO -- how do we print progress?
         //printProgress(dataProvider.getShard(), ???);
 
         return result;
     }
 
+    @Override
+    public void printOnTraversalDone() {
+        nanoScheduler.shutdown();
+        super.printOnTraversalDone();    //To change body of overridden methods use File | Settings | File Templates.
+    }
+
     private static class NotImplementedReadReferenceView extends ReadReferenceView {
         private NotImplementedReadReferenceView(ShardDataProvider provider) {
             super(provider);

public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java

@@ -136,7 +136,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
 
     private void debugPrint(final String format, Object ... args) {
         if ( isDebug() )
-            logger.info(String.format(format, args));
+            logger.info("Thread " + Thread.currentThread().getId() + ":" + String.format(format, args));
     }
 
 
@@ -205,7 +205,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
                                             final MapFunction<InputType, MapType> map,
                                             final ReduceType initialValue,
                                             final ReduceFunction<MapType, ReduceType> reduce) {
-        debugPrint("Executing nanoScheduler with initial reduce value " + initialValue);
+        debugPrint("Executing nanoScheduler");
         ReduceType sum = initialValue;
         while ( inputReader.hasNext() ) {
             try {