[med-svn] [picard-tools] 05/07: apply patch on new CBZip2 calls, constructor is different, I selected the False for the headerless parameter in InputStream constructor

[Olivier Sallou]

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

commit 50fbf3176fec183c280fca5fad3e6b36dd38e38c
Author: Olivier Sallou <olivier.sallou at debian.org>
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);

-- 
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