Incorporating clover into build.xml
-- See http://gatkforums.broadinstitute.org/discussion/2002/clover-coverage-analysis-with-ant for use docs -- Fix for artificial reads not having proper read groups, causing NPE in some tests -- Added clover itself to private/resources
This commit is contained in:
Mark DePristo
parent
7796ba7601
commit
14944b5d73
50
build.xml
50
build.xml
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@ -107,7 +107,7 @@
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<!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
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<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
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<property name="test.default.maxmemory" value="4g"/>
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<!-- ******************************************************************************** -->
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<!-- Filesets and paths -->
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@ -267,19 +267,19 @@
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<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
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<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
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dest="${ivy.jar.dir}/${ivy.jar.file}"
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usetimestamp="true"/>
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<taskdef resource="org/apache/ivy/ant/antlib.xml"
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uri="antlib:org.apache.ivy.ant"
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classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
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<!-- <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}" -->
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<!-- dest="${ivy.jar.dir}/${ivy.jar.file}" -->
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<!-- usetimestamp="true"/> -->
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<!-- <taskdef resource="org/apache/ivy/ant/antlib.xml" -->
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<!-- uri="antlib:org.apache.ivy.ant" -->
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<!-- classpath="${ivy.jar.dir}/${ivy.jar.file}"/> -->
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<get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
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dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
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usetimestamp="true"/>
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<taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
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uri="antlib:antlib:org.apache.maven.artifact.ant"
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classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
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<!-- <get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}" -->
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<!-- dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}" -->
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<!-- usetimestamp="true"/> -->
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<!-- <taskdef resource="org/apache/maven/artifact/ant/antlib.xml" -->
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<!-- uri="antlib:antlib:org.apache.maven.artifact.ant" -->
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<!-- classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/> -->
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<!-- End network lines -->
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@ -596,6 +596,7 @@
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<path id="doclet.classpath">
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<path refid="external.dependencies" />
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<pathelement location="${java.classes}" />
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<pathelement location="${clover.jar}" />
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</path>
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<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
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@ -1038,6 +1039,7 @@
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<delete dir="${staging.dir}"/>
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<delete dir="${dist.dir}"/>
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<delete dir="${pipelinetest.dir}"/>
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<clover-clean/>
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</target>
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<!-- Depend on this target if your target requires a clean working directory but you don't want to depend on clean directly -->
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@ -1090,7 +1092,6 @@
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<property name="iwww.report.dir" value="${user.home}/private_html/report"/>
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<property name="test.output" value="${dist.dir}/test"/>
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<property name="testng.jar" value="${lib.dir}/testng-5.14.1.jar"/>
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<property name="test.maxmemory" value="4g"/> <!-- provide a ceiling on the memory that unit/integration tests can consume. -->
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<path id="java.test.source.path">
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<dirset dir="${basedir}">
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@ -1119,8 +1120,12 @@
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</fileset>
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</path>
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<property name="clover.jar" location="private/resources/clover/lib/clover.jar"/>
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<taskdef resource="cloverlib.xml" classpath="${clover.jar}"/>
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<path id="testng.default.classpath">
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<path refid="build.results" />
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<pathelement path="${clover.jar}"/>
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<pathelement location="${java.contracts.dir}" />
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<pathelement location="${java.test.classes}" />
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<pathelement location="${scala.test.classes}" />
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@ -1128,6 +1133,17 @@
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<!-- Test targets -->
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<target name="clover.report">
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<clover-html-report outdir="clover_html" title="GATK Clover report"/>
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</target>
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<target name="with.clover">
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<clover-setup fullyQualifyJavaLang="true" instrumentationLevel="method">
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</clover-setup>
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<property name="compile.scala" value="false" /> <!-- currently doesn't work with scala -->
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<property name="test.maxmemory" value="32g"/> <!-- clover requires lots of memory -->
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</target>
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<target name="test.init.compile">
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<mkdir dir="${java.test.classes}"/>
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<mkdir dir="${scala.test.classes}"/>
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@ -1207,6 +1223,7 @@
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<echo message="Test Classpath: ${test.classpath.display.string}" />
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<echo message="" />
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<echo message="Sting: Running @{testtype} test cases!"/>
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<echo message="Test Memory : ${test.maxmemory}" />
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<!-- no test is allowed to run for more than 10 hours -->
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<taskdef resource="testngtasks" classpath="${testng.jar}"/>
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@ -1220,10 +1237,11 @@
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listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.TestNGTestTransformer,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
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<jvmarg value="-Xmx${test.maxmemory}" />
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<jvmarg value="-ea" />
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<jvmarg value="-Dclover.pertest.coverage=diff" />
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<jvmarg value="-Djava.awt.headless=true" />
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<jvmarg value="-Dpipeline.run=${pipeline.run}" />
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<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
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<jvmarg line="${cofoja.jvm.args}"/>
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<!-- <jvmarg line="${cofoja.jvm.args}"/> -->
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<jvmarg line="${debug.jvm.args}"/>
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<!-- NOTE: To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
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@ -1262,6 +1280,7 @@
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<target name="test.init">
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<property name="testng.classpath" value="testng.default.classpath" />
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<property name="test.maxmemory" value="${test.default.maxmemory}"/>
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</target>
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<target name="init.testgatkjar">
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@ -1374,6 +1393,7 @@
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<!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
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<!-- Usage: ant fasttest -Dsingle=TestClass -->
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<target name="fasttest" depends="init.javaonly,init">
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<property name="test.maxmemory" value="${test.default.maxmemory}"/>
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<condition property="not.clean">
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<and>
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<available file="${build.dir}" />
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@ -131,7 +131,7 @@ public class GATKRunReport {
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private String hostName;
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@Element(required = true, name = "java")
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private String java;
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private String javaVersion;
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@Element(required = true, name = "machine")
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private String machine;
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@ -212,7 +212,7 @@ public class GATKRunReport {
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hostName = Utils.resolveHostname();
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// basic java information
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java = Utils.join("-", Arrays.asList(System.getProperty("java.vendor"), System.getProperty("java.version")));
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javaVersion = Utils.join("-", Arrays.asList(System.getProperty("java.vendor"), System.getProperty("java.version")));
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machine = Utils.join("-", Arrays.asList(System.getProperty("os.name"), System.getProperty("os.arch")));
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// if there was an exception, capture it
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@ -188,6 +188,7 @@ public class ArtificialSAMUtils {
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GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
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rec.setReadBases(bases);
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rec.setBaseQualities(qual);
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rec.setReadGroup(new GATKSAMReadGroupRecord("x"));
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if (refIndex == -1) {
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rec.setReadUnmappedFlag(true);
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}
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