diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java
index f9861a717..e04f55e87 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java
@@ -89,7 +89,7 @@ public class UnsignedIntPackedInputStream {
 
         int i = 0;
         while(i < length)
-            data[offset+i++] = readBuffer.getInt();
+            data[offset+i++] = readBuffer.getInt() & 0xFFFFFFFFL;
     }
 
     /**