When reducing multiple samples it is possible to try to close a region that for a given sample has no reads. Currently we'd NPE. Fixed.

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java

@@ -80,7 +80,7 @@ public class SingleSampleCompressor {
     }
 
     public Set<GATKSAMRecord> closeVariantRegions(CompressionStash regions) {
-        return slidingWindow.closeVariantRegions(regions);
+        return slidingWindow == null ? Collections.<GATKSAMRecord>emptySet() : slidingWindow.closeVariantRegions(regions);
     }
 
 }