[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 3772b109e00b8bdf8531731bc7c73009ff6cd147
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Wed Apr 10 16:30:56 2013 +0200

    add cofoja to classpath

diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 76009a7..615f631 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -25,17 +25,18 @@ Forwarded: no
  
      <property environment="env"/>
  
-@@ -72,6 +72,9 @@
+@@ -72,6 +72,10 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
 +            <pathelement path="/usr/share/java/testng.jar"/>
 +            <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/>
 +            <pathelement path="/usr/share/java/jbzip2.jar"/>
++            <pathelement path="/usr/share/java/cofoja.jar"/>
          </path>
          <path  id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -209,7 +212,7 @@
+@@ -209,7 +213,7 @@
          <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"/>
-@@ -239,6 +242,8 @@
+@@ -239,6 +243,8 @@
          </copy>
      </target>
  

-- 
manipulate SAM and BAM files