NanoScheduler tracks time within input, map, and reduce

-- Helpful for understanding where the time goes to each bit of the code.
-- Controlled by a local static boolean, to avoid the potential overhead in general

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

@@ -3,6 +3,8 @@ package org.broadinstitute.sting.utils.nanoScheduler;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.AutoFormattingTime;
+import org.broadinstitute.sting.utils.SimpleTimer;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
@@ -44,6 +46,7 @@ import java.util.concurrent.*;
 public class NanoScheduler<InputType, MapType, ReduceType> {
     private final static Logger logger = Logger.getLogger(NanoScheduler.class);
     private final static boolean ALLOW_SINGLE_THREAD_FASTPATH = true;
+    private final static boolean TIME_CALLS = true;
 
     final int bufferSize;
     final int nThreads;
@@ -51,6 +54,10 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
     boolean shutdown = false;
     boolean debug = false;
 
+    final SimpleTimer inputTimer = new SimpleTimer();
+    final SimpleTimer mapTimer = new SimpleTimer();
+    final SimpleTimer reduceTimer = new SimpleTimer();
+
     /**
      * Create a new nanoschedule with the desire characteristics requested by the argument
      *
@@ -97,6 +104,19 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
                 throw new IllegalStateException("Remaining tasks found in the executor, unexpected behavior!");
         }
         shutdown = true;
+
+        if (TIME_CALLS) {
+            printTimerInfo("Input  time", inputTimer);
+            printTimerInfo("Map    time", mapTimer);
+            printTimerInfo("Reduce time", reduceTimer);
+        }
+    }
+
+    private void printTimerInfo(final String label, final SimpleTimer timer) {
+        final double total = inputTimer.getElapsedTime() + mapTimer.getElapsedTime() + reduceTimer.getElapsedTime();
+        final double myTimeInSec = timer.getElapsedTime();
+        final double myTimePercent = myTimeInSec / total * 100;
+        logger.info(String.format("%s: %s (%5.2f%%)", label, new AutoFormattingTime(myTimeInSec), myTimePercent));
     }
 
     /**
@@ -134,10 +154,10 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
      * It is safe to call this function repeatedly on a single nanoScheduler, at least until the
      * shutdown method is called.
      *
-     * @param inputReader
+     * @param inputReader an iterator providing us with the input data to nanoSchedule map/reduce over
-     * @param map
+     * @param map the map function from input type -> map type, will be applied in parallel to each input
-     * @param reduce
+     * @param reduce the reduce function from map type + reduce type -> reduce type to be applied in order to map results
-     * @return
+     * @return the last reduce value
      */
     public ReduceType execute(final Iterator<InputType> inputReader,
                               final MapFunction<InputType, MapType> map,
@@ -213,7 +233,10 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
         // while mapQueue has something in it to reduce
         for ( final Future<MapType> future : mapQueue ) {
             final MapType value = future.get(); // block until we get the values for this task
+
+            if ( TIME_CALLS) reduceTimer.restart();
             sum = reduce.apply(value, sum);
+            if ( TIME_CALLS) reduceTimer.stop();
         }
 
         return sum;
@@ -229,11 +252,15 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
     private List<InputType> readInputs(final Iterator<InputType> inputReader) {
         int n = 0;
         final List<InputType> inputs = new LinkedList<InputType>();
+
+        if ( TIME_CALLS) inputTimer.restart();
         while ( inputReader.hasNext() && n < getBufferSize() ) {
             final InputType input = inputReader.next();
             inputs.add(input);
             n++;
         }
+        if ( TIME_CALLS) inputTimer.stop();
+
         return inputs;
     }
 
@@ -266,7 +293,10 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
         }
 
         @Override public MapType call() throws Exception {
-            return map.apply(input);
+            if ( TIME_CALLS) mapTimer.restart();
+            final MapType result = map.apply(input);
+            if ( TIME_CALLS) mapTimer.stop();
+            return result;
         }
     }
 }