Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter

-- The progress meter isn't started until the GATK actually calls execute on the microscheduler.  Now we get a message saying "Creating shard strategy" while this (expensive) operation runs

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -271,7 +271,9 @@ public class GenomeAnalysisEngine {
         // create the output streams
         initializeOutputStreams(microScheduler.getOutputTracker());
 
+        logger.info("Creating shard strategy for " + readsDataSource.getReaderIDs().size() + " BAM files");
         Iterable<Shard> shardStrategy = getShardStrategy(readsDataSource,microScheduler.getReference(),intervals);
+        logger.info("Done creating shard strategy");
 
         // execute the microscheduler, storing the results
         return microScheduler.execute(this.walker, shardStrategy);

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

@@ -139,6 +139,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
     }
 
     public Object execute( Walker walker, Iterable<Shard> shardStrategy ) {
+        super.startingExecution();
+
         // Fast fail for walkers not supporting TreeReducible interface.
         if (!( walker instanceof TreeReducible ))
             throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");

public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -80,6 +80,7 @@ public class LinearMicroScheduler extends MicroScheduler {
      * @param shardStrategy A strategy for sharding the data.
      */
     public Object execute(Walker walker, Iterable<Shard> shardStrategy) {
+        super.startingExecution();
         walker.initialize();
         Accumulator accumulator = Accumulator.create(engine,walker);
 

public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -300,6 +300,17 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
      */
     public abstract Object execute(Walker walker, Iterable<Shard> shardStrategy);
 
+    /**
+     * Tells this MicroScheduler that the execution of one of the subclass of this object as started
+     *
+     * Must be called when the implementation of execute actually starts up
+     *
+     * Currently only starts the progress meter timer running, but other start up activities could be incorporated
+     */
+    protected void startingExecution() {
+        progressMeter.start();
+    }
+
     /**
      * Retrieves the object responsible for tracking and managing output.
      * @return An output tracker, for loading data in and extracting results.  Will not be null.

public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java

@@ -154,6 +154,8 @@ public class ProgressMeter {
     /**
      * Create a new ProgressMeter
      *
+     * Note that progress meter isn't started until the client calls start()
+     *
      * @param performanceLogFile an optional performance log file where a table of performance logs will be written
      * @param processingUnitName the name of the unit type being processed, suitable for saying X seconds per processingUnitName
      * @param processingIntervals the intervals being processed
@@ -193,7 +195,6 @@ public class ProgressMeter {
 
         // start up the timer
         progressMeterDaemon = new ProgressMeterDaemon(this, pollingFrequency);
-        start();
     }
 
     public ProgressMeterDaemon getProgressMeterDaemon() {
@@ -205,7 +206,7 @@ public class ProgressMeter {
      * daemon thread for periodic printing.
      */
     @Requires("progressMeterDaemon != null")
-    private synchronized void start() {
+    public synchronized void start() {
         timer.start();
         lastProgressPrintTime = timer.currentTime();
 

public/java/test/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java

@@ -63,6 +63,7 @@ public class ProgressMeterDaemonUnitTest extends BaseTest {
 
         private TestingProgressMeter(final long poll) {
             super(null, "test", new GenomeLocSortedSet(genomeLocParser), poll);
+            super.start();
         }
 
         @Override