diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
index 77a3a666f..036d2782a 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
@@ -50,6 +50,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.sam.AlignmentStartWithNoTiesComparator;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
+import java.util.Collections;
 import java.util.Set;
 import java.util.TreeSet;
 
@@ -126,7 +127,7 @@ public class SingleSampleCompressor {
     }
 
     public Set<GATKSAMRecord> closeVariantRegions(CompressionStash regions) {
-        return slidingWindow.closeVariantRegions(regions);
+        return slidingWindow == null ? Collections.<GATKSAMRecord>emptySet() : slidingWindow.closeVariantRegions(regions);
     }
 
 }