Author: Andreas Tille <tille@debian.org>
        Emmanuel Bourg <ebourg@apache.org>
Last-Update: Fri Dec 4 19:18:21 2015 +0100
Description: Use Debian packaged JARs

--- a/build.xml
+++ b/build.xml
@@ -11,9 +11,10 @@
     <property name="source" value="1.5"/>
     <path id="FastQC.classpath">
         <pathelement location="bin"/>
-        <pathelement location="jbzip2-0.9.jar"/>
-        <pathelement location="sam-1.103.jar"/>
-        <pathelement location="cisd-jhdf5.jar"/>
+        <pathelement location="/usr/share/java/jbzip2.jar"/>
+        <pathelement location="/usr/share/java/htsjdk.jar"/>
+        <pathelement location="/usr/share/java/sis-jhdf5.jar"/>
+        <pathelement location="/usr/share/java/commons-math3.jar"/>
     </path>
     <target name="init">
         <mkdir dir="bin"/>
@@ -34,6 +35,7 @@
         <echo message="${ant.project.name}: ${ant.file}"/>
         <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
             <src path="."/>
+            <exclude name=".pc/**"/>
             <classpath refid="FastQC.classpath"/>
         </javac>
     </target>