The following commit has been merged in the master branch: commit 2b649574317a70acec5182442c24959198d36ee6 Author: Olivier Sallou <olivier.sal...@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 <sjack...@debian.org>, Charles Plessy <ple...@debian.org>, Olivier Sallou <osal...@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 <osal...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit