From 839c5d66bc8592bed3d9da1f67c1078249de267d Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 15 Oct 2009 16:15:11 +0000
Subject: [PATCH] Read uints directly into longs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1853 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../alignment/bwa/packing/UnsignedIntPackedInputStream.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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;
     }
 
     /**