This is an automated email from the git hooks/post-receive script. osallou pushed a commit to branch master in repository picard-tools.
commit 50fbf3176fec183c280fca5fad3e6b36dd38e38c Author: Olivier Sallou <[email protected]> Date: Tue Dec 24 11:30:12 2013 +0100 apply patch on new CBZip2 calls, constructor is different, I selected the False for the headerless parameter in InputStream constructor --- debian/patches/use_libjbzip2-java | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/debian/patches/use_libjbzip2-java b/debian/patches/use_libjbzip2-java index 1e4e215..d991f79 100644 --- a/debian/patches/use_libjbzip2-java +++ b/debian/patches/use_libjbzip2-java @@ -18,18 +18,27 @@ Forwarded: not-needed /** * A class for utility methods that wrap or aggregate functionality in Java IO. -@@ -237,7 +237,7 @@ +@@ -232,12 +232,12 @@ + + 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); ++ return new BZip2InputStream(fis, false); } catch (IOException ioe) { throw new PicardException("Error opening file: " + file.getName(), ioe); -@@ -346,7 +346,7 @@ +@@ -344,9 +344,9 @@ + 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 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); -- 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
