[med-svn] [SCM] picard-tools branch, master, updated. upstream/1.55-53-g9ff5425

[Charles Plessy]

The following commit has been merged in the master branch:
commit 23976b3c1762adcaafd2465bef355518147104e9
Author: Charles Plessy <plessy at debian.org>
Date:   Thu Apr 5 13:05:49 2012 +0900

    Refreshed patch, use Debian's snappy-java.

diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 03b6716..e7888cf 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -5,8 +5,8 @@ Description: Modifies the upstream build system.
  from src/scripts/net/sf/picard/analysis/.
 Origin: vendor
 Forwarded: no
---- picard-tools.orig/build.xml
-+++ picard-tools/build.xml
+--- a/build.xml
++++ b/build.xml
 @@ -23,7 +23,7 @@
    ~ THE SOFTWARE.
    -->
@@ -16,36 +16,40 @@ Forwarded: no
  
      <property name="src" value="src/java"/>
      <property name="src.scripts" value="src/scripts"/>
-@@ -74,6 +74,7 @@
+@@ -60,6 +60,8 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
 +            <pathelement path="/usr/share/java/testng.jar"/>
++            <pathelement path="/usr/share/java/snappy-java.jar"/>
          </path>
          <path  id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -108,7 +109,7 @@
+@@ -92,7 +94,8 @@
+                debug="${javac.debug}"
                 sourcepath="" srcdir="${src}"
                 includes ="net/sf/samtools/**/*.*"
-                excludes = "net/sf/picard/**/*.*"
--               executable="${JAVA_HOME_1_5}/bin/javac"
-+               executable="javac"
-                compiler="javac1.5" fork="true">
+-               excludes = "net/sf/picard/**/*.*">
++               excludes = "net/sf/picard/**/*.*"
++               executable="javac">
              <!--<compilerarg value="-Xlint:all"/>-->
              <!--<compilerarg value="-Xlint:unchecked"/>-->
-@@ -137,7 +138,7 @@
+             <classpath refid="classpath"/>
+@@ -119,7 +122,8 @@
+         <javac destdir="${classes.test}"
                 optimize="${javac.opt}"
                 debug="${javac.debug}"
-                includes ="net/sf/samtools/**/*.*"
--               executable="${JAVA_HOME_1_5}/bin/javac"
-+               executable="javac"
-                compiler="javac1.5" fork="true"> <!-- Force SAM-JDK to be built with 1.5 -->
+-               includes ="net/sf/samtools/**/*.*">
++               includes ="net/sf/samtools/**/*.*"
++               executable="javac">
              <!--<compilerarg value="-Xlint:unchecked"/>-->
              <src path="${src.test}"/>
-@@ -221,9 +222,12 @@
+             <classpath>
+@@ -206,10 +210,12 @@
          <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
              <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
+-            <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
 +            <fileset dir="${src.scripts}" includes="**/*.R"/>
          </jar>
      </target>

-- 
manipulate SAM and BAM files