[med-svn] [SCM] picard-tools branch, master, updated. debian/1.82-1-9-g231fd2a

[Olivier Sallou]

The following commit has been merged in the master branch:
commit 0000348f2cd411aa46da769b62c9fdda44af2d52
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Wed Apr 10 16:26:50 2013 +0200

    update pathc to new release

diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 76b7ed8..76009a7 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -16,7 +16,16 @@ Forwarded: no
  
      <property name="src" value="src/java"/>
      <property name="src.scripts" value="src/scripts"/>
-@@ -63,6 +63,9 @@
+@@ -51,7 +51,7 @@
+     <property name="command_tmp" value=".command_tmp"/>
+     <property name="command-line-html-dir" value="${dist}/html"/>
+     <property name="testng.verbosity" value="2"/>
+-    <property name="contracts.jar" value="${lib}/cofoja-1.0-r139.jar"/>
++    <property name="contracts.jar" value="/usr/share/java/cofoja.jar"/>
+ 
+     <property environment="env"/>
+ 
+@@ -72,6 +72,9 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
@@ -26,17 +35,7 @@ Forwarded: no
          </path>
          <path  id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -122,7 +125,8 @@
-         <javac destdir="${classes.test}"
-                optimize="${javac.opt}"
-                debug="${javac.debug}"
--               includes ="net/sf/samtools/**/*.*">
-+               includes ="net/sf/samtools/**/*.*"
-+               executable="javac">
-             <!--<compilerarg value="-Xlint:unchecked"/>-->
-             <src path="${src.test}"/>
-             <classpath>
-@@ -213,7 +217,7 @@
+@@ -209,7 +212,7 @@
          <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
              <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
@@ -45,8 +44,8 @@ Forwarded: no
              <manifest>
                  <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
                  <attribute name="Implementation-Vendor" value="Broad Institute"/>
-@@ -221,6 +225,8 @@
-         </jar>
+@@ -239,6 +242,8 @@
+         </copy>
      </target>
  
 +<target name="jar" depends="sam-jar, picard-jar" />

-- 
manipulate SAM and BAM files