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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
