[Debian-med-packaging] [SCM] picard-tools branch, master, updated. upstream/1.26-23-g342a25c

[Charles Plessy]

The following commit has been merged in the master branch:
commit 342a25c251614b6a8d84de04079da24c3af6e26c
Author: Charles Plessy <plessy at debian.org>
Date:   Thu Jul 22 14:23:22 2010 +0900

    * New upstream release; refreshed Debian patch.

diff --git a/debian/changelog b/debian/changelog
index 9c749cb..6611cef 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,6 @@
-picard-tools (1.25-2) UNRELEASED; urgency=low
+picard-tools (1.26-1) UNRELEASED; urgency=low
 
+  * New upstream release.
   * Removed the fourth number in Standards-Version (debian/control,
     see Policy §5.6.11).
 
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 7d0603b..6215e2a 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-1.25.orig/build.xml
-+++ picard-tools-1.25/build.xml
+--- picard-tools.orig/build.xml
++++ picard-tools/build.xml
 @@ -23,7 +23,7 @@
    ~ THE SOFTWARE.
    -->
@@ -16,7 +16,7 @@ Forwarded: no
  
      <property name="src" value="src/java"/>
      <property name="src.scripts" value="src/scripts"/>
-@@ -63,6 +63,7 @@
+@@ -74,6 +74,7 @@
              <fileset dir="${lib}">
                  <include name="**/*.jar"/>
              </fileset>
@@ -24,7 +24,7 @@ Forwarded: no
          </path>
          <path  id="metrics.classpath">
              <pathelement path="${classpath}"/>
-@@ -97,7 +98,7 @@
+@@ -108,7 +109,7 @@
                 sourcepath="" srcdir="${src}"
                 includes ="net/sf/samtools/**/*.*"
                 excludes = "net/sf/picard/**/*.*"
@@ -33,7 +33,7 @@ Forwarded: no
                 compiler="javac1.5" fork="true">
              <!--<compilerarg value="-Xlint:all"/>-->
              <!--<compilerarg value="-Xlint:unchecked"/>-->
-@@ -126,7 +127,7 @@
+@@ -137,7 +138,7 @@
                 optimize="${javac.opt}"
                 debug="${javac.debug}"
                 includes ="net/sf/samtools/**/*.*"
@@ -42,7 +42,7 @@ Forwarded: no
                 compiler="javac1.5" fork="true"> <!-- Force SAM-JDK to be built with 1.5 -->
              <!--<compilerarg value="-Xlint:unchecked"/>-->
              <src path="${src.test}"/>
-@@ -203,9 +204,12 @@
+@@ -214,9 +215,12 @@
          <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
              <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>

-- 
manipulate SAM and BAM files