build.xml

<project name="THetA" default="distJars" basedir=".">
    <description>
        Build jar file for THetA code
    </description>
  <!-- set global properties for this build -->

  <property name="srcTHetA" location="java/src" />
  <property name="buildTHetA" location="java/build" />
  <property name="dist" location="bin"/>
  <property name="lib" location="jarfiles"/>

  <!-- include external jars -->
  <path id="THetA.classpath">
	  <fileset dir="${lib}" >
		  <include name="sam-1.78.jar"/>
	  </fileset>
  </path>
  
  
  <target name="clean"
        description="clean up" >
    <!-- Delete the ${build} directory tree -->
    <delete dir="${build}"/>
    <!-- <delete dir="${dist}"/> -->
  </target>

  <target name="init" depends="clean">
    <!-- Create the time stamp -->
    <tstamp/>
    <!-- Create the build directory structure used by compile -->
    <mkdir dir="${buildTHetA}"/>
    <mkdir dir="${dist}"/>
  </target>

  <target name="compileTHetA" depends="init"
        description="compile the source " >
    <!-- Compile the java code from ${srcTHetA} into ${buildTHetA} -->
    <javac srcdir="${srcTHetA}" includeantruntime="false" classpathref="THetA.classpath" destdir="${buildTHetA}"/>
  </target>

  <target name="distBuildBICToTHetA" depends="compileTHetA"
	  description="generate the distribution runBICToTHetA.jar" >

	<!-- make jar file -->
	<jar jarfile="${dist}/runBICSeqToTHetA.jar" basedir="${buildTHetA}">
		<manifest>
			<attribute name="Main-Class" value="BICSeqToTHetA"/>
		</manifest>
	</jar>
 </target>

 <target name="distBuildAlleleCounts" depends="distBuildBICToTHetA"
	 description="generate the distribution getAlleleCoutns.jar" >

	 <!-- make jar file -->
	 <jar jarfile="${dist}/getAlleleCounts.jar" basedir="${buildTHetA}">
		 
		<zipgroupfileset dir="${lib}" includes="*.jar" />
		<manifest>
			<attribute name="Main-Class" value="getAlleleCounts"/>
		 </manifest>
	 </jar>
 </target>

  <target name="distJars" depends="distBuildAlleleCounts"
        description="generates all jar files" >
  </target>

</project>