Enable control of reporting periodicity

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java

@@ -52,6 +52,9 @@ public class GATKArgumentCollection {
     // the default value of the stop of the expanded window
     public static final int DEFAULT_REFERENCE_WINDOW_STOP = 0;
 
+    // the default time in seconds between progress meter calls
+    public final static long DEFAULT_SECONDS_BETWEEN_PROGRESS_UPDATES = 10;
+
     /** the constructor */
     public GATKArgumentCollection() {
     }
@@ -354,6 +357,10 @@ public class GATKArgumentCollection {
     @Argument(fullName = "globalQScorePrior", shortName = "globalQScorePrior", doc = "Global Qscore Bayesian prior to use for BQSR", required = false)
     public double globalQScorePrior = -1.0;
 
+    @Advanced
+    @Argument(fullName="secondsBetweenProgressUpdates", shortName = "secondsBetweenProgressUpdates", doc = "Time interval for process meter information output (in seconds)", required=false)
+    public long secondsBetweenProgressUpdates = DEFAULT_SECONDS_BETWEEN_PROGRESS_UPDATES;
+
 
     // --------------------------------------------------------------------------------------------------------------
     //

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java

@@ -204,7 +204,8 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
         // Create the progress meter, and register it with the analysis engine
         engine.registerProgressMeter(new ProgressMeter(progressLogFile,
                 availableTraversalEngines.peek().getTraversalUnits(),
-                engine.getRegionsOfGenomeBeingProcessed()));
+                engine.getRegionsOfGenomeBeingProcessed(),
+                engine.getArguments().secondsBetweenProgressUpdates));
 
         // Now that we have a progress meter, go through and initialize the traversal engines
         for ( final TraversalEngine traversalEngine : allCreatedTraversalEngines )

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java

@@ -170,22 +170,15 @@ 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
+     * @param secondsBetweenProgressUpdates how frequently (in seconds) to print progress
      */
     public ProgressMeter(final File performanceLogFile,
-                         final String processingUnitName,
-                         final GenomeLocSortedSet processingIntervals) {
-        this(performanceLogFile, processingUnitName, processingIntervals, ProgressMeterDaemon.DEFAULT_POLL_FREQUENCY_MILLISECONDS);
-    }
-
-    protected ProgressMeter(final File performanceLogFile,
                             final String processingUnitName,
                             final GenomeLocSortedSet processingIntervals,
-                            final long pollingFrequency) {
+                            final long secondsBetweenProgressUpdates) {
         if ( processingUnitName == null ) throw new IllegalArgumentException("processingUnitName cannot be null");
         if ( processingIntervals == null ) throw new IllegalArgumentException("Target intervals cannot be null");
 
@@ -212,7 +205,7 @@ public class ProgressMeter {
         targetSizeInBP = processingIntervals.coveredSize();
 
         // start up the timer
-        progressMeterDaemon = new ProgressMeterDaemon(this, pollingFrequency);
+        progressMeterDaemon = new ProgressMeterDaemon(this, secondsBetweenProgressUpdates);
     }
 
     public ProgressMeterDaemon getProgressMeterDaemon() {

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.gatk.utils.progressmeter;
 
+import java.util.concurrent.TimeUnit;
+
 /**
  * Daemon thread that periodically prints the progress of the progress meter
  *
@@ -33,20 +35,10 @@ package org.broadinstitute.gatk.utils.progressmeter;
  * Time: 9:16 PM
  */
 public final class ProgressMeterDaemon extends Thread {
-    public final static long DEFAULT_POLL_FREQUENCY_MILLISECONDS = 10 * 1000;
-
     /**
      * How frequently should we poll and print progress?
      */
-    private final long pollFrequencyMilliseconds;
+    private final long secondsBetweenProgressUpdates;
-
-    /**
-     * How long are we waiting between print progress calls are issued?
-     * @return the time in milliseconds between progress meter calls
-     */
-    private long getPollFrequencyMilliseconds() {
-        return pollFrequencyMilliseconds;
-    }
 
     /**
      * Are we to continue periodically printing status, or should we shut down?
@@ -60,22 +52,19 @@ public final class ProgressMeterDaemon extends Thread {
 
     /**
      * Create a new ProgressMeterDaemon printing progress for meter
-     * @param meter the progress meter to print progress of
+     * @param meter the progress meter to print progress
+     * @param secondsBetweenProgressUpdates how frequently (in seconds) to print progress
      */
-    public ProgressMeterDaemon(final ProgressMeter meter, final long pollFrequencyMilliseconds) {
+    public ProgressMeterDaemon(final ProgressMeter meter, final long secondsBetweenProgressUpdates) {
         if ( meter == null ) throw new IllegalArgumentException("meter cannot be null");
-        if ( pollFrequencyMilliseconds <= 0 ) throw new IllegalArgumentException("pollFrequencyMilliseconds must be greater than 0 but got " + pollFrequencyMilliseconds);
+        if ( secondsBetweenProgressUpdates <= 0 ) throw new IllegalArgumentException("secondsBetweenProgressUpdates must be greater than 0 but got " + secondsBetweenProgressUpdates);
 
         this.meter = meter;
-        this.pollFrequencyMilliseconds = pollFrequencyMilliseconds;
+        this.secondsBetweenProgressUpdates = secondsBetweenProgressUpdates;
         setDaemon(true);
         setName("ProgressMeterDaemon");
     }
 
-    public ProgressMeterDaemon(final ProgressMeter meter) {
-        this(meter, DEFAULT_POLL_FREQUENCY_MILLISECONDS);
-    }
-
     /**
      * Tells this daemon thread to shutdown at the next opportunity, as the progress
      * metering is complete.
@@ -102,7 +91,7 @@ public final class ProgressMeterDaemon extends Thread {
             meter.printProgress(false);
             meter.updateElapsedTimeInNanoseconds();
             try {
-                Thread.sleep(getPollFrequencyMilliseconds());
+                Thread.sleep(TimeUnit.SECONDS.toMillis(secondsBetweenProgressUpdates));
             } catch (InterruptedException e) {
                 throw new RuntimeException(e);
             }