Remove endOfInput check from submit method implementations.

src/main/java/org/broadinstitute/hellbender/utils/downsampling/PositionalDownsampler.java

@@ -30,13 +30,6 @@ public final class PositionalDownsampler extends ReadsDownsampler {
 
     private List<GATKRead> finalizedReads;
 
-    /**
-     * Reads may be submitted until signalEndOfInput is called, after which no more reads may be submitted unless
-     * one of {@link #consumeFinalizedItems()} or {@link #clearItems()} is called to reset the internal state of
-     * the downsampler.
-     */
-    private boolean endOfInputStream;
-
     /**
      * Construct a PositionalDownsampler
      *
@@ -46,7 +39,6 @@ public final class PositionalDownsampler extends ReadsDownsampler {
     public PositionalDownsampler( final int targetCoverage, final SAMFileHeader header ) {
         Utils.validateArg(targetCoverage > 0, "targetCoverage must be > 0");
         Utils.nonNull(header);
-        Utils.validate(! endOfInputStream, "attempt to submit read after end of input stream has been signaled");
 
         this.reservoir = new ReservoirDownsampler(targetCoverage);
         this.finalizedReads = new ArrayList<>();
@@ -148,7 +140,6 @@ public int size() {
 
     @Override
     public void signalEndOfInput() {
-        endOfInputStream = true;
         finalizeReservoir(false);
     }
 
@@ -157,7 +148,6 @@ public void clearItems() {
         reservoir.clearItems();
         reservoir.resetStats();
         finalizedReads.clear();
-        endOfInputStream = false;
         previousRead = null;
     }
 

src/main/java/org/broadinstitute/hellbender/utils/downsampling/ReservoirDownsampler.java

@@ -95,9 +95,6 @@ public ReservoirDownsampler(final int targetSampleSize ) {
     @Override
     public void submit ( final GATKRead newRead ) {
         Utils.nonNull(newRead, "newRead");
-        // Once the end of the input stream has been seen, consumeFinalizedItems or clearItems must be called to
-        // reset the state of the ReservoirDownsampler before more items can be submitted
-        Utils.validate(! endOfInputStream, "attempt to submit read after end of input stream has been signaled");
 
         // Only count reads that are actually eligible for discarding for the purposes of the reservoir downsampling algorithm
         totalReadsSeen++;