[med-svn] [picard-tools] 04/07: but back patch erased by error

[Olivier Sallou]

This is an automated email from the git hooks/post-receive script.

osallou pushed a commit to branch master
in repository picard-tools.

commit 71a6fbd18bdf5925f765870c5070f6158273161c
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Tue Dec 24 11:23:38 2013 +0100

    but back patch erased by error
---
 debian/patches/use_libjbzip2-java | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/debian/patches/use_libjbzip2-java b/debian/patches/use_libjbzip2-java
index 28f8850..1e4e215 100644
--- a/debian/patches/use_libjbzip2-java
+++ b/debian/patches/use_libjbzip2-java
@@ -18,3 +18,21 @@ Forwarded: not-needed
  
  /**
   * A class for utility methods that wrap or aggregate functionality in Java IO.
+@@ -237,7 +237,7 @@
+                 throw new PicardException(file.getAbsolutePath() + " is not a BZIP file.");
+             }
+ 
+-            return new CBZip2InputStream(fis);
++            return new BZip2InputStream(fis);
+         }
+         catch (IOException ioe) {
+             throw new PicardException("Error opening file: " + file.getName(), ioe);
+@@ -346,7 +346,7 @@
+             final FileOutputStream fos = new FileOutputStream(file, append);
+             fos.write(66); //write magic number 'BZ' because CBZip2OutputStream does not do it for you
+             fos.write(90);
+-            return new BufferedOutputStream(new CBZip2OutputStream(fos), Defaults.BUFFER_SIZE);
++            return new BufferedOutputStream(new BZip2OutputStream(fos), Defaults.BUFFER_SIZE);
+         }
+         catch (IOException ioe) {
+             throw new PicardException("Error opening file for writing: " + file.getName(), ioe);

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git