Pushing traversal engine timer start to as close to actual start as possible

-- Should make initial timings more accurate

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

@@ -44,7 +44,6 @@ public class LinearMicroScheduler extends MicroScheduler {
      * @param shardStrategy A strategy for sharding the data.
      */
     public Object execute(Walker walker, ShardStrategy shardStrategy) {
-        traversalEngine.startTimers();
         walker.initialize();
         Accumulator accumulator = Accumulator.create(engine,walker);
 
@@ -54,6 +53,7 @@ public class LinearMicroScheduler extends MicroScheduler {
             if ( done || shard == null ) // we ran out of shards that aren't owned
                 break;
 
+            traversalEngine.startTimersIfNecessary();
             if(shard.getShardType() == Shard.ShardType.LOCUS) {
                 LocusWalker lWalker = (LocusWalker)walker;
                 WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleMetadata());

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

@@ -57,6 +57,7 @@ public class ShardTraverser implements Callable {
 
     public Object call() {
         try {
+            traversalEngine.startTimersIfNecessary();
             long startTime = System.currentTimeMillis();
 
             Object accumulator = walker.reduceInit();

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

@@ -115,7 +115,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
     LinkedList<ProcessingHistory> history = new LinkedList<ProcessingHistory>();
 
     /** We use the SimpleTimer to time our run */
-    private SimpleTimer timer = new SimpleTimer("Traversal");
+    private SimpleTimer timer = null;
 
     // How long can we go without printing some progress info?
     private static final int PRINT_PROGRESS_CHECK_FREQUENCY_IN_CYCLES = 1000;
@@ -209,11 +209,16 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
         }
     }
     /**
-     * Should be called to indicate that we're going to process records and the timer should start ticking
+     * Should be called to indicate that we're going to process records and the timer should start ticking.  This
+     * function should be called right before any traversal work is done, to avoid counting setup costs in the
+     * processing costs and inflating the estimated runtime.
      */
-    public void startTimers() {
-        timer.start();
-        lastProgressPrintTime = timer.currentTime();
+    public void startTimersIfNecessary() {
+        if ( timer == null ) {
+            timer = new SimpleTimer("Traversal");
+            timer.start();
+            lastProgressPrintTime = timer.currentTime();
+        }
     }
 
     /**