[med-svn] [picard-tools] 03/07: adapt patch to latest release

[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 ad07325274b888069f0ef520216ed3261b1f7ff7
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Tue Dec 24 11:21:03 2013 +0100

    adapt patch to latest release
---
 debian/patches/use_libjbzip2-java | 31 ++-----------------------------
 1 file changed, 2 insertions(+), 29 deletions(-)

diff --git a/debian/patches/use_libjbzip2-java b/debian/patches/use_libjbzip2-java
index 38dddb8..28f8850 100644
--- a/debian/patches/use_libjbzip2-java
+++ b/debian/patches/use_libjbzip2-java
@@ -7,10 +7,10 @@ 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
-@@ -33,8 +33,8 @@
- import java.util.regex.Pattern;
+@@ -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;
@@ -18,30 +18,3 @@ Forwarded: not-needed
  
  /**
   * A class for utility methods that wrap or aggregate functionality in Java IO.
-@@ -230,12 +230,12 @@
- 
-         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);
-@@ -342,9 +342,9 @@
-         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 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