The following commit has been merged in the master branch:
commit 3772b109e00b8bdf8531731bc7c73009ff6cd147
Author: Olivier Sallou <[email protected]>
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
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