[med-svn] [SCM] picard-tools branch, master, updated. debian/1.90-3-7-g53b7a12

[Olivier Sallou]

The following commit has been merged in the master branch:
commit 46ead8f8a974d35e99df2978341deefaa09c3f44
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Thu Jul 25 14:32:14 2013 +0200

    include broad related files in picard jar file

diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index d462572..d8f7ab3 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -28,15 +28,18 @@ Forwarded: no
          </path>
          <path  id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -195,7 +200,6 @@
+@@ -194,8 +199,9 @@
+         <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
              <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
++            <fileset dir="${classes}" includes="org/broad/tribble/**/*.*"/>
++            <fileset dir="${classes}" includes="org/broadinstitute/variant/**/*.*"/>
              <fileset dir="${src.scripts}" includes="**/*.R"/>
 -            <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
              <manifest>
                  <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
                  <attribute name="Implementation-Vendor" value="Broad Institute"/>
-@@ -225,6 +229,8 @@
+@@ -225,6 +231,8 @@
          </copy>
      </target>
  

-- 
manipulate SAM and BAM files