Add size() method to Downsampler interface

-- This method provides client with the current number of elements, without having to retreive the underlying list<T>.  Added unit tests for LevelingDownsampler and ReservoirDownsampler as these are the only two complex ones.  All of the others are trivially obviously correct.

public/java/src/org/broadinstitute/sting/gatk/downsampling/Downsampler.java

@@ -94,6 +94,17 @@ public interface Downsampler<T> {
      */
     public T peekPending();
 
+    /**
+     * Get the current number of items in this downsampler
+     *
+     * This should be the best estimate of the total number of elements that will come out of the downsampler
+     * were consumeFinalizedItems() to be called immediately after this call.  In other words it should
+     * be number of finalized items + estimate of number of pending items that will ultimately be included as well.
+     *
+     * @return a positive integer
+     */
+    public int size();
+
     /**
      * Returns the number of items discarded (so far) during the downsampling process
      *

public/java/src/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java

@@ -109,6 +109,11 @@ public class FractionalDownsampler<T extends SAMRecord> implements ReadsDownsamp
         return numDiscardedItems;
     }
 
+    @Override
+    public int size() {
+        return selectedReads.size();
+    }
+
     public void signalEndOfInput() {
         // NO-OP
     }

public/java/src/org/broadinstitute/sting/gatk/downsampling/LevelingDownsampler.java

@@ -128,6 +128,15 @@ public class LevelingDownsampler<T extends List<E>, E> implements Downsampler<T>
         return numDiscardedItems;
     }
 
+    @Override
+    public int size() {
+        int s = 0;
+        for ( final List<E> l : groups ) {
+            s += l.size();
+        }
+        return s;
+    }
+
     public void signalEndOfInput() {
         levelGroups();
         groupsAreFinalized = true;

public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java

@@ -89,6 +89,11 @@ public class PassThroughDownsampler<T extends SAMRecord> implements ReadsDownsam
         return 0;
     }
 
+    @Override
+    public int size() {
+        return selectedReads.size();
+    }
+
     public void signalEndOfInput() {
         // NO-OP
     }

public/java/src/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java

@@ -156,6 +156,11 @@ public class ReservoirDownsampler<T extends SAMRecord> implements ReadsDownsampl
         return numDiscardedItems;
     }
 
+    @Override
+    public int size() {
+        return reservoir.size();
+    }
+
     public void signalEndOfInput() {
         // NO-OP
     }

public/java/src/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java

@@ -112,6 +112,11 @@ public class SimplePositionalDownsampler<T extends SAMRecord> implements ReadsDo
         return numDiscardedItems;
     }
 
+    @Override
+    public int size() {
+        return finalizedReads.size() + reservoir.size();
+    }
+
     public void signalEndOfInput() {
         finalizeReservoir();
     }

public/java/test/org/broadinstitute/sting/gatk/downsampling/LevelingDownsamplerUnitTest.java

@@ -139,6 +139,7 @@ public class LevelingDownsamplerUnitTest extends BaseTest {
             Assert.assertTrue(downsampler.peekFinalized() == null && downsampler.peekPending() == null);
         }
 
+        final int sizeFromDownsampler = downsampler.size();
         List<List<Object>> downsampledStacks = downsampler.consumeFinalizedItems();
         Assert.assertFalse(downsampler.hasFinalizedItems() || downsampler.hasPendingItems());
         Assert.assertTrue(downsampler.peekFinalized() == null && downsampler.peekPending() == null);
@@ -151,6 +152,7 @@ public class LevelingDownsamplerUnitTest extends BaseTest {
             totalRemainingItems += stack.size();
         }
 
+        Assert.assertEquals(sizeFromDownsampler, totalRemainingItems);
         int numItemsReportedDiscarded = downsampler.getNumberOfDiscardedItems();
         int numItemsActuallyDiscarded = test.numStacks * test.stackSize - totalRemainingItems;
 

public/java/test/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java

@@ -115,6 +115,7 @@ public class ReservoirDownsamplerUnitTest extends BaseTest {
             Assert.assertTrue(downsampler.peekFinalized() == null && downsampler.peekPending() == null);
         }
 
+        Assert.assertEquals(downsampler.size(), test.expectedNumReadsAfterDownsampling);
         List<SAMRecord> downsampledReads = downsampler.consumeFinalizedItems();
         Assert.assertFalse(downsampler.hasFinalizedItems() || downsampler.hasPendingItems());
         Assert.assertTrue(downsampler.peekFinalized() == null && downsampler.peekPending() == null);