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build.xml
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build.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- WARNING: Eclipse auto-generated file.
Any modifications will be overwritten.
To include a user specific buildfile here, simply create one in the same
directory with the processing instruction <?eclipse.ant.import?>
as the first entry and export the buildfile again. -->
<project basedir="." default="build" name="SequenceAnalysis" xmlns:jacoco="antlib:org.jacoco.ant">
<taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml">
<classpath path="lib_build_run_test/org.jacoco.ant-0.7.5.201505241946.jar:lib_build_run_test/org.jacoco.core-0.7.5.201505241946.jar:lib_build_run_test/org.jacoco.report-0.7.5.201505241946.jar:lib_build_run_test/org.jacoco.agent-0.7.5.201505241946.jar:lib_build_run_test/asm-debug-all-5.0.4.jar"/>
</taskdef>
<target name="jacoco:report">
<jacoco:report>
<executiondata>
<file file="target/jacoco.exec"/>
</executiondata>
<structure name="Mutinack">
<classfiles>
<fileset dir="bin">
<exclude name="**/picard/**"/>
<exclude name="**/samtools/**"/>
<exclude name="**/PosByPosNumbersPB*"/>
</fileset>
</classfiles>
<sourcefiles encoding="UTF-8">
<fileset dir="src"/>
</sourcefiles>
</structure>
<html destdir="target/site/jacoco"/>
</jacoco:report>
</target>
<property name="jmh.jar" location="lib_build_run_test/jmh-core-1.20-SNAPSHOT.jar"/>
<property name="jmh-generator-annprocess.jar" location="lib_build_run_test/jmh-generator-annprocess-1.20-SNAPSHOT.jar"/>
<property name="build.compiler" value="extJavac"/>
<property environment="env"/>
<property name="junit.output.dir" value="junit"/>
<property name="debuglevel" value="source,lines,vars"/>
<property name="target" value="1.8"/>
<property name="source" value="1.8"/>
<import file="build-user.xml"/>
<path id="SequenceAnalysis.classpath">
<pathelement location="bin"/>
<pathelement location="lib/jcommander-1.33-SNAPSHOT.jar"/>
<pathelement location="lib/org.eclipse.jdt.annotation_2.0.0.v20131221-0104_beta_java8.jar"/>
<pathelement location="lib_build_run_test/junit-4.12.jar"/>
<pathelement location="lib/trove.jar"/>
<pathelement location="lib/eclipse-collections-8.2.0-SNAPSHOT.jar"/>
<pathelement location="lib/eclipse-collections-api-8.2.0-SNAPSHOT.jar"/>
<pathelement location="lib/bzip2.jar"/>
<pathelement location="lib/snappy-java-1.0.3-rc3.jar"/>
<pathelement location="lib_build_run_test/hamcrest-core-1.3.jar"/>
<pathelement location="lib/slf4j-api-1.7.7.jar"/>
<pathelement location="lib/logback-core-1.1.3.jar"/>
<pathelement location="lib/logback-classic-1.1.3.jar"/>
<pathelement location="lib/protobuf-java-2.4.1_PATCHED.jar"/>
<pathelement location="lib_build_run_test/equalsverifier-1.7.6.jar"/>
<pathelement location="lib_build_run_test/jmockit-1.21.jar"/>
<pathelement location="findbugs-3.0.1/lib/findbugs.jar"/>
<pathelement location="lib/commons-io-2.4.jar"/>
<pathelement location="lib_build_run_test/pitest-1.1.8.jar"/>
<pathelement location="lib/jackson-core-2.7.0.jar"/>
<pathelement location="lib/jackson-databind-2.7.0.jar"/>
<pathelement location="lib/jackson-annotations-2.7.0.jar"/>
<pathelement location="lib/fst-2.43-onejar.jar"/>
<pathelement location="lib/rmiio-2.1.3-SNAPSHOT.jar"/>
<pathelement location="lib/xchart-3.3.1-SNAPSHOT.jar"/>
<pathelement location="lib/xz-1.8.jar"/>
<pathelement location="${jmh.jar}"/>
<pathelement location="${jmh-generator-annprocess.jar}"/>
<pathelement location="lib_build_run_test/jdo-api-3.1.jar"/>
<pathelement location="lib_build_run_test/javax.jdo-3.2.0-m7-SNAPSHOT.jar"/>
<pathelement location="lib_build_run_test/javax.persistence-2.2.0-m2-SNAPSHOT.jar"/>
<pathelement location="lib_build_run_test/datanucleus-api-jdo-5.0.6-SNAPSHOT.jar"/>
<pathelement location="lib_build_run_test/datanucleus-core-5.0.7-SNAPSHOT.jar"/>
<pathelement location="lib_build_run_test/datanucleus-rdbms-5.0.6-SNAPSHOT.jar"/>
<pathelement location="lib_build_run_test/final_annotation.jar"/>
</path>
<target name="init">
<mkdir dir="bin"/>
<copy includeemptydirs="false" todir="bin">
<fileset dir="src">
<exclude name="**/*.java*"/>
<exclude name="contrib/net/sf/picard/vcf/"/>
</fileset>
</copy>
</target>
<target name="clean">
<delete dir="bin"/>
<delete dir="{junit.output.dir}" failonerror="false"/>
<delete file="target/jacoco.exec"/>
</target>
<target name="clean_main">
<delete dir="bin/uk/org/cinquin"/>
<delete dir="{junit.output.dir}" failonerror="false"/>
</target>
<target depends="clean" name="cleanall"/>
<target depends="build-subprojects,build-project" name="build"/>
<target name="build-subprojects"/>
<path id="errorprone">
<fileset dir="lib_build_run_test" includes="error_prone_ant*.jar"/>
</path>
<path id="final-annotation-processor">
<fileset dir="." includes="final_annotation_processor.jar"/>
<path refid="SequenceAnalysis.classpath"/>
</path>
<target depends="init" name="build-with-final-fields">
<javac encoding="ISO-8859-1" debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
<compilerarg value="-XDignore.symbol.file"/>
<src path="src"/>
<include name="uk/org/cinquin/**/*.java"/>
<classpath refid="final-annotation-processor"/>
</javac>
</target>
<target depends="init" name="build-project">
<echo message="${ant.project.name}: ${ant.file}"/>
<javac encoding="ISO-8859-1" debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
<compilerarg value="-XDignore.symbol.file"/>
<compilerarg value="-parameters"/>
<src path="src"/>
<include name="contrib/edu/**/*.java"/>
<include name="contrib/net/**/*.java"/>
<include name="contrib/com/jcraft/**/*.java"/>
<include name="**/*PB.java"/>
<include name="contrib/jdk/**/*.java"/>
<classpath refid="SequenceAnalysis.classpath"/>
<compilerclasspath refid="errorprone"/>
</javac>
<javac compiler="com.google.errorprone.ErrorProneAntCompilerAdapter" encoding="ISO-8859-1" debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
<compilerarg value="-XDignore.symbol.file"/>
<compilerarg value="-parameters"/>
<compilerarg value="-Xep:Finally:OFF"/>
<compilerarg value="-Xep:StringSplitter:OFF"/>
<compilerarg value="-Xep:CatchAndPrintStackTrace:OFF"/>
<compilerarg value="-Xep:DefaultCharset:OFF"/>
<compilerarg value="-XepDisableWarningsInGeneratedCode"/>
<src path="src"/>
<classpath refid="SequenceAnalysis.classpath"/>
<compilerclasspath refid="errorprone"/>
</javac>
</target>
<target name="UtilTest">
<delete dir="{junit.output.dir}" failonerror="false"/>
<mkdir dir="${junit.output.dir}"/>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.misc_util.UtilTest" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
</target>
<target name="FunctionalTests">
<delete dir="{junit.output.dir}" failonerror="false"/>
<mkdir dir="${junit.output.dir}"/>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<jvmarg value="-XX:CompileCommand=exclude,gnu.trove.impl.hash.TObjectHash::insertKey"/>
<jvmarg value="-XX:CompileCommand=exclude,gnu.trove.impl.hash.TIntHash::insertKey"/>
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.tests.FunctionalTestRerun" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
</target>
<target name="SequenceAnalysis" depends="build">
<mkdir dir="${junit.output.dir}"/>
<parallel>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="contrib.nf.fr.eraasoft.pool.test.TestPool" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.features.tests.BedReaderTest" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.features.tests.GenomeIntervalTest" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.misc_util.UtilTest" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.statistics.CounterTest" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.tests.TestEqualsHashcodeContracts" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<formatter type="xml"/>
<test name="uk.org.cinquin.mutinack.tests.TestEqualsHashcodeContractsParametrized" todir="${junit.output.dir}"/>
<classpath refid="SequenceAnalysis.classpath"/>
</junit>
</jacoco:coverage>
<jacoco:coverage destfile="target/jacoco.exec">
<junit fork="yes" printsummary="withOutAndErr">
<classpath refid="SequenceAnalysis.classpath"/>
<batchtest todir="${junit.output.dir}">
<fileset dir="bin/">
<include name="uk/org/cinquin/mutinack/tests/*Test.class" />
</fileset>
</batchtest>
<formatter type="xml"/>
</junit>
</jacoco:coverage>
</parallel>
</target>
<target depends="SequenceAnalysis" name="junitreport">
<junitreport todir="${junit.output.dir}">
<fileset dir="${junit.output.dir}">
<include name="TEST-*.xml"/>
</fileset>
<report format="frames" todir="${junit.output.dir}"/>
</junitreport>
</target>
</project>