Subject: use libjbzip2-java classes
Description: Debian package for this class
 is libjbzip2-java, need to update package
 name
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2012-08-31
Forwarded: not-needed
--- a/src/java/htsjdk/samtools/cram/io/ExternalCompression.java
+++ b/src/java/htsjdk/samtools/cram/io/ExternalCompression.java
@@ -5,7 +5,7 @@ import htsjdk.samtools.util.IOUtil;
 import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
 import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
 import org.apache.commons.compress.compressors.xz.XZCompressorOutputStream;
-import org.apache.tools.bzip2.CBZip2InputStream;
+import org.itadaki.bzip2.BZip2InputStream;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -74,7 +74,7 @@ public class ExternalCompression {
         // hello, apache!
         byteArrayInputStream.read();
         byteArrayInputStream.read();
-        return InputStreamUtils.readFully(new CBZip2InputStream(byteArrayInputStream));
+        return InputStreamUtils.readFully(new BZip2InputStream(byteArrayInputStream, false));
     }
 
     /**
