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/net/sf/picard/io/IoUtil.java
+++ b/src/java/net/sf/picard/io/IoUtil.java
@@ -35,8 +35,8 @@
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
 
-import org.apache.tools.bzip2.CBZip2InputStream;
-import org.apache.tools.bzip2.CBZip2OutputStream;
+import org.itadaki.bzip2.BZip2InputStream;
+import org.itadaki.bzip2.BZip2OutputStream;
 
 /**
  * A class for utility methods that wrap or aggregate functionality in Java IO.
@@ -235,12 +235,12 @@
 
         try {
             final FileInputStream fis = new FileInputStream(file);
-            if(fis.read() != 66 || fis.read() != 90) { //Read magic number 'BZ' or else CBZip2InputStream will complain about it
+            if(fis.read() != 66 || fis.read() != 90) { //Read magic number 'BZ' or else BZip2InputStream will complain about it
                 fis.close();
                 throw new PicardException(file.getAbsolutePath() + " is not a BZIP file.");
             }
 
-            return new CBZip2InputStream(fis);
+            return new BZip2InputStream(fis, false);
         }
         catch (IOException ioe) {
             throw new PicardException("Error opening file: " + file.getName(), ioe);
@@ -351,9 +351,9 @@
         try {
 
             final FileOutputStream fos = new FileOutputStream(file, append);
-            fos.write(66); //write magic number 'BZ' because CBZip2OutputStream does not do it for you
+            fos.write(66); //write magic number 'BZ' because BZip2OutputStream does not do it for you
             fos.write(90);
-            return IOUtil.maybeBufferOutputStream(new CBZip2OutputStream(fos));
+            return IOUtil.maybeBufferOutputStream(new BZip2OutputStream(fos));
         }
         catch (IOException ioe) {
             throw new PicardException("Error opening file for writing: " + file.getName(), ioe);
