[med-svn] [picard-tools] 05/06: Refreshed patch for upstream version 1.110.

[Charles Plessy]

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

commit 33d232d044074ccc77b280c16534014a92c4cbce
Author: Charles Plessy <plessy at debian.org>
Date:   Sun Apr 6 10:55:49 2014 +0900

    Refreshed patch for upstream version 1.110.
---
 debian/patches/use_libjbzip2-java | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/debian/patches/use_libjbzip2-java b/debian/patches/use_libjbzip2-java
index d991f79..f8d9570 100644
--- a/debian/patches/use_libjbzip2-java
+++ b/debian/patches/use_libjbzip2-java
@@ -18,7 +18,7 @@ Forwarded: not-needed
  
  /**
   * A class for utility methods that wrap or aggregate functionality in Java IO.
-@@ -232,12 +232,12 @@
+@@ -235,12 +235,12 @@
  
          try {
              final FileInputStream fis = new FileInputStream(file);
@@ -33,15 +33,15 @@ Forwarded: not-needed
          }
          catch (IOException ioe) {
              throw new PicardException("Error opening file: " + file.getName(), ioe);
-@@ -344,9 +344,9 @@
+@@ -351,9 +351,9 @@
          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);
+-            return IOUtil.maybeBufferOutputStream(new CBZip2OutputStream(fos));
++            return IOUtil.maybeBufferOutputStream(new BZip2OutputStream(fos));
          }
          catch (IOException ioe) {
              throw new PicardException("Error opening file for writing: " + file.getName(), ioe);

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