diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
index ba6321121..bf5f33dc3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
@@ -59,7 +59,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
      */
     public FilePointer next() {
         FilePointer current = wrappedIterator.next();
-        while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0)
+        while(wrappedIterator.hasNext() && current.isRegionUnmapped == wrappedIterator.peek().isRegionUnmapped && current.minus(wrappedIterator.peek()) == 0)
             current = current.combine(parser,wrappedIterator.next());
         return current;
     }