[med-svn] [SCM] picard-tools branch, master, updated. upstream/1.75-58-gfd50413

[Olivier Sallou]

The following commit has been merged in the master branch:
commit fd504130c64984cd459b7644db4141e2c2887761
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Tue Aug 28 14:28:56 2012 +0200

    update patches to latests version

diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index bf424a4..dca49d9 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -16,45 +16,39 @@ Forwarded: no
  
      <property name="src" value="src/java"/>
      <property name="src.scripts" value="src/scripts"/>
-@@ -60,6 +60,8 @@
+@@ -63,6 +63,8 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
 +            <pathelement path="/usr/share/java/testng.jar"/>
 +            <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/>
          </path>
-         <path  id="metrics.classpath">
+         <path id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -92,7 +94,8 @@
-                debug="${javac.debug}"
-                sourcepath="" srcdir="${src}"
-                includes ="net/sf/samtools/**/*.*"
--               excludes = "net/sf/picard/**/*.*">
-+               excludes = "net/sf/picard/**/*.*"
-+               executable="javac">
-             <!--<compilerarg value="-Xlint:all"/>-->
-             <!--<compilerarg value="-Xlint:unchecked"/>-->
-             <classpath refid="classpath"/>
-@@ -119,7 +122,8 @@
+@@ -123,7 +125,8 @@
          <javac destdir="${classes.test}"
                 optimize="${javac.opt}"
                 debug="${javac.debug}"
--               includes ="net/sf/samtools/**/*.*">
-+               includes ="net/sf/samtools/**/*.*"
+-               includes="net/sf/samtools/**/*.*">
++               includes="net/sf/samtools/**/*.*"
 +               executable="javac">
              <!--<compilerarg value="-Xlint:unchecked"/>-->
              <src path="${src.test}"/>
              <classpath>
-@@ -206,10 +210,12 @@
+@@ -214,7 +217,7 @@
          <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
-             <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
+             <fileset dir="${classes}" includes="net/sf/picard/**/*.*"/>
 -            <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
 +            <fileset dir="${src.scripts}" includes="**/*.R"/>
+             <manifest>
+                 <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
+                 <attribute name="Implementation-Vendor" value="Broad Institute"/>
+@@ -222,6 +225,8 @@
          </jar>
      </target>
  
-+    <target name="jar" depends="sam-jar, picard-jar" />
++<target name="jar" depends="sam-jar, picard-jar" />
 +
      <target name="javadoc" depends="init" description="Generates the project javadoc.">
          <javadoc

-- 
manipulate SAM and BAM files