[med-svn] [SCM] picard-tools branch, master, updated. upstream/1.75-62-g2b64957

[Olivier Sallou]

The following commit has been merged in the master branch:
commit 2b649574317a70acec5182442c24959198d36ee6
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Fri Aug 31 09:45:58 2012 +0200

    add patch to use libjbzip2-java

diff --git a/debian/control b/debian/control
index fa61ebc..7e7f521 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Uploaders: Shaun Jackman <sjackman at debian.org>,
  Charles Plessy <plessy at debian.org>,
  Olivier Sallou <osallou at debian.org>
 Build-Depends: ant, default-jdk, testng, libsnappy1.0.3-java,
- debhelper (>= 7.0.50~)
+ debhelper (>= 7.0.50~), libjbzip2-java
 Standards-Version: 3.9.3
 Homepage: http://picard.sourceforge.net/
 Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index dca49d9..66f3a07 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -16,16 +16,17 @@ Forwarded: no
  
      <property name="src" value="src/java"/>
      <property name="src.scripts" value="src/scripts"/>
-@@ -63,6 +63,8 @@
+@@ -63,6 +63,9 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
 +            <pathelement path="/usr/share/java/testng.jar"/>
 +            <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/>
++            <pathelement path="/usr/share/java/jbzip2.jar"/>
          </path>
          <path id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -123,7 +125,8 @@
+@@ -123,7 +126,8 @@
          <javac destdir="${classes.test}"
                 optimize="${javac.opt}"
                 debug="${javac.debug}"
@@ -35,7 +36,7 @@ Forwarded: no
              <!--<compilerarg value="-Xlint:unchecked"/>-->
              <src path="${src.test}"/>
              <classpath>
-@@ -214,7 +217,7 @@
+@@ -214,7 +218,7 @@
          <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
              <fileset dir="${classes}" includes="net/sf/picard/**/*.*"/>
@@ -44,7 +45,7 @@ Forwarded: no
              <manifest>
                  <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
                  <attribute name="Implementation-Vendor" value="Broad Institute"/>
-@@ -222,6 +225,8 @@
+@@ -222,6 +226,8 @@
          </jar>
      </target>
  
diff --git a/debian/patches/series b/debian/patches/series
index 5f585a1..24b6ad5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+use_libjbzip2-java
 01-build.xml
diff --git a/debian/patches/use_libjbzip2-java b/debian/patches/use_libjbzip2-java
new file mode 100644
index 0000000..38dddb8
--- /dev/null
+++ b/debian/patches/use_libjbzip2-java
@@ -0,0 +1,47 @@
+Subject: use libjbzip2-java classes
+Description: Debian package for this class
+ is libjbzip2-java, need to update package
+ name
+Author: Olivier Sallou <osallou at debian.org>
+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;
+ 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;
++import org.itadaki.bzip2.BZip2OutputStream;
+ 
+ /**
+  * 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);

-- 
manipulate SAM and BAM files