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Merge remote-tracking branch 'unstable/master'

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2 parents d785397 + 7a7adb7 commit 3ce0a32da7fa141050c433725b9e05bfb4ca4a32 @eitanbanks eitanbanks committed Feb 26, 2013
Showing 1,472 changed files with 72,882 additions and 61,652 deletions.
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@@ -12,6 +12,7 @@
*.ipr
*.iws
*.iml
+*.pyc
.DS_Store
queueScatterGather
/foo*
@@ -23,3 +24,4 @@ dist/
dump/
lib/
out/
+/atlassian-ide-plugin.xml
View
126 build.xml
@@ -107,7 +107,12 @@
<!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
+ <property name="test.default.maxmemory" value="4g"/>
+ <!-- clover parameters -->
+ <property name="clover.jar" location="private/resources/clover/lib/clover.jar"/>
+ <property name="clover.instrument.level" value="method"/>
+ <taskdef resource="cloverlib.xml" classpath="${clover.jar}"/>
<!-- ******************************************************************************** -->
<!-- Filesets and paths -->
@@ -596,6 +601,7 @@
<path id="doclet.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
+ <pathelement location="${clover.jar}" />
</path>
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
@@ -644,12 +650,8 @@
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
<jar jarfile="${dist.dir}/StingUtils.jar">
- <fileset dir="${java.classes}">
- <include name="**/utils/**/*.class"/>
- <exclude name="**/utils/codecs/vcf/**/*.class"/>
- <exclude name="**/utils/variantcontext/**/*.class"/>
- </fileset>
- <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
+ <fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
+ <fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
@@ -659,26 +661,14 @@
<include name="**/${R.package.path}/**/*.tar.gz"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
- <include name="**/utils/**/*.R"/>
+ <include name="**/sting/utils/**/*.R"/>
</fileset>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
</manifest>
</jar>
</target>
- <target name="vcf.jar" depends="gatk.compile,init.jar">
- <jar jarfile="${dist.dir}/vcf.jar">
- <fileset dir="${java.classes}">
- <include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
- <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
- <include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
- <include name="org/broadinstitute/sting/utils/exceptions/**"/>
- <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
- </fileset>
- </jar>
- </target>
-
<target name="na12878kb.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/na12878kb.jar">
<fileset dir="${java.classes}">
@@ -703,12 +693,12 @@
<fileset dir="${java.contracts.dir}" />
<fileset dir="${java.classes}">
<include name="${resource.file}" />
- <include name="**/gatk/**/*.class" />
- <include name="**/alignment/**/*.class"/>
+ <include name="**/sting/gatk/**/*.class" />
+ <include name="**/sting/alignment/**/*.class"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
- <include name="**/gatk/**/*.R"/>
- <include name="**/alignment/**/*.R"/>
+ <include name="**/sting/gatk/**/*.R"/>
+ <include name="**/sting/alignment/**/*.R"/>
</fileset>
<fileset dir="${key.dir}">
<include name="**/*.key"/>
@@ -719,7 +709,7 @@
</jar>
<jar jarfile="${dist.dir}/Aligner.jar">
- <fileset dir="${java.classes}" includes="**/alignment/**/*.class" />
+ <fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
</jar>
<subant target="dist" genericantfile="build.xml">
@@ -755,7 +745,7 @@
</jar>
</target>
- <target name="sting.jar" depends="sting-utils.jar, vcf.jar, gatk.jar, queue.jar" />
+ <target name="sting.jar" depends="sting-utils.jar, gatk.jar, queue.jar" />
<target name="init.manifests" depends="sting.jar">
<pathconvert property="jar.classpath" pathsep=" ">
@@ -875,10 +865,6 @@
<property name="executable" value="GenomeAnalysisTK" />
</target>
- <target name="init.executable.gatklite" depends="init.build.publiconly, init.javaonly">
- <property name="executable" value="GenomeAnalysisTKLite" />
- </target>
-
<target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
<property name="executable" value="Queue" />
</target>
@@ -887,10 +873,6 @@
<property name="executable" value="Queue" />
</target>
- <target name="init.executable.queuelite" depends="init.build.publiconly, init.javaandscala">
- <property name="executable" value="QueueLite" />
- </target>
-
<target name="require.executable">
<condition property="no.executable.defined">
<or>
@@ -941,15 +923,10 @@
<!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="package.gatk.full" depends="init.executable.gatkfull,package" />
- <target name="package.gatk.lite" depends="init.executable.gatklite,package" />
-
<target name="package.queue.all" depends="init.executable.queueall,package" />
<target name="package.queue.full" depends="init.executable.queuefull,package" />
- <target name="package.queue.lite" depends="init.executable.queuelite,package" />
-
-
<!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
<target name="release" depends="require.executable" description="release a build, putting each file in a location specified by the package">
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
@@ -958,13 +935,8 @@
<!-- Release specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="release.gatk.full" depends="package.gatk.full,release" />
- <target name="release.gatk.lite" depends="package.gatk.lite,release" />
-
<target name="release.queue.full" depends="package.queue.full,release" />
- <target name="release.queue.lite" depends="package.queue.lite,release" />
-
-
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
<!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
<target name="build-picard-private" depends="resolve">
@@ -993,7 +965,7 @@
<!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
<target name="mvninstall" depends="package" description="maven install a package into .m2/repository">
- <property name="mvn.build.version" value="0.0.1" />
+ <property name="mvn.build.version" value="0.0.2" />
<!--
We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
<property name="mvn.build.version" value="${build.version}" />
@@ -1008,14 +980,10 @@
<!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
- <target name="mvninstall.gatk.lite" depends="package.gatk.lite,mvninstall" />
-
<target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
<target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
- <target name="mvninstall.queue.lite" depends="package.queue.lite,mvninstall" />
-
<!-- ******************************************************************************** -->
<!-- Clean -->
<!-- ******************************************************************************** -->
@@ -1032,14 +1000,22 @@
<delete dir="${scaladoc.dir}" />
</target>
+ <target name="-check.clover">
+ <available property="clover.installed" classname="com.cenqua.clover.CloverInstr" />
+ </target>
+
+ <target name="clean.clover" depends="-check.clover" if="clover.installed">
+ <clover-clean/>
+ </target>
+
<target name="clean.gsalib">
<!-- Currently not cleaning out the lib during 'ant clean' -->
<exec executable="R" failonerror="false">
<arg line="R CMD REMOVE gsalib" />
</exec>
</target>
- <target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs">
+ <target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs,clean.clover">
<delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/>
<delete dir="${contract.dump.dir}"/>
@@ -1097,8 +1073,7 @@
<property name="report" value="${build.dir}/report"/>
<property name="iwww.report.dir" value="${user.home}/private_html/report"/>
<property name="test.output" value="${dist.dir}/test"/>
- <property name="testng.jar" value="${lib.dir}/testng-5.14.1.jar"/>
- <property name="test.maxmemory" value="4g"/> <!-- provide a ceiling on the memory that unit/integration tests can consume. -->
+ <property name="testng.jar" value="${lib.dir}/testng-6.8.jar"/>
<path id="java.test.source.path">
<dirset dir="${basedir}">
@@ -1129,13 +1104,53 @@
<path id="testng.default.classpath">
<path refid="build.results" />
+ <pathelement path="${clover.jar}"/>
<pathelement location="${java.contracts.dir}" />
<pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" />
</path>
<!-- Test targets -->
+ <target name="clover.report">
+ <clover-report coverageCacheSize="nocache">
+ <current outfile="clover_html" title="GATK clover report" showUniqueCoverage="false" numThreads="4">
+ <format type="html" filter="catch,static,property"/>
+ <fileset dir="public">
+ <patternset id="clover.excludes">
+ <exclude name="**/*UnitTest.java"/>
+ <exclude name="**/*TestProvider*.java"/>
+ <exclude name="**/*PerformanceTest.java"/>
+ <exclude name="**/*Benchmark.java"/>
+ <exclude name="**/*LargeScaleTest.java"/>
+ <exclude name="**/*IntegrationTest.java"/>
+ <exclude name="**/jna/**/*.java"/>
+ <exclude name="**/queue/extensions/**/*.java"/>
+ <exclude name="**/sting/utils/help/*.java"/>
+ <exclude name="**/sting/tools/*.java"/>
+ <exclude name="**/datasources/reads/utilities/*.java"/>
+ <exclude name="**/sting/alignment/**/*.java"/>
+ <exclude name="**/examples/**/*.java"/>
+ </patternset>
+ </fileset>
+ <fileset dir="private">
+ <patternset refid="clover.excludes" />
+ </fileset>
+ <fileset dir="protected">
+ <patternset refid="clover.excludes" />
+ </fileset>
+ </current>
+ </clover-report>
+ </target>
+
+ <target name="with.clover">
+ <clover-setup fullyQualifyJavaLang="true" instrumentationLevel="${clover.instrument.level}">
+ </clover-setup>
+ <property name="compile.scala" value="false" /> <!-- currently doesn't work with scala -->
+ <property name="test.maxmemory" value="32g"/> <!-- clover requires lots of memory -->
+ <echo message="Clover instrument level: ${clover.instrument.level}" />
+ </target>
+
<target name="test.init.compile">
<mkdir dir="${java.test.classes}"/>
<mkdir dir="${scala.test.classes}"/>
@@ -1215,6 +1230,7 @@
<echo message="Test Classpath: ${test.classpath.display.string}" />
<echo message="" />
<echo message="Sting: Running @{testtype} test cases!"/>
+ <echo message="Test Memory : ${test.maxmemory}" />
<!-- no test is allowed to run for more than 10 hours -->
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
@@ -1228,6 +1244,7 @@
listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.TestNGTestTransformer,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
<jvmarg value="-Xmx${test.maxmemory}" />
<jvmarg value="-ea" />
+ <jvmarg value="-Dclover.pertest.coverage=diff" />
<jvmarg value="-Djava.awt.headless=true" />
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
@@ -1270,6 +1287,7 @@
<target name="test.init">
<property name="testng.classpath" value="testng.default.classpath" />
+ <property name="test.maxmemory" value="${test.default.maxmemory}"/>
</target>
<target name="init.testgatkjar">
@@ -1315,13 +1333,8 @@
<!-- Order of the dependencies is significant in the *.release.tests targets -->
<target name="gatkfull.binary.release.tests" depends="init.usecontracts,package.gatk.full,init.testgatkjar,unittest,integrationtest" />
- <target name="gatklite.binary.release.tests" depends="init.usecontracts,package.gatk.lite,init.testgatkjar,unittest,integrationtest" />
-
<target name="queuefull.binary.release.tests" depends="init.usecontracts,package.queue.full,init.testqueuejar,pipelinetest" />
- <target name="queuelite.binary.release.tests" depends="init.usecontracts,package.queue.lite,init.testqueuejar,pipelinetest" />
-
-
<!-- Our four different test types: UnitTest, IntegrationTest, LargeScaleTest, PipelineTest -->
<target name="unittest" depends="test.compile,test.init" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">
@@ -1382,6 +1395,7 @@
<!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
<!-- Usage: ant fasttest -Dsingle=TestClass -->
<target name="fasttest" depends="init.javaonly,init">
+ <property name="test.maxmemory" value="${test.default.maxmemory}"/>
<condition property="not.clean">
<and>
<available file="${build.dir}" />
View
@@ -35,6 +35,9 @@
<!-- Tribble -->
<dependency org="org.broad" name="tribble" rev="latest.integration"/>
+ <!-- Variant -->
+ <dependency org="org.broadinstitute" name="variant" rev="latest.integration"/>
+
<dependency org="log4j" name="log4j" rev="1.2.15"/>
<dependency org="javax.mail" name="mail" rev="1.4.4"/>
<dependency org="colt" name="colt" rev="1.2.0"/>
@@ -61,6 +64,7 @@
<dependency org="commons-lang" name="commons-lang" rev="2.5"/>
<dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
<dependency org="commons-io" name="commons-io" rev="2.1"/>
+ <dependency org="commons-collections" name="commons-collections" rev="3.2.1"/>
<dependency org="org.apache.commons" name="commons-math" rev="2.2"/>
<!-- Lucene core utilities -->
@@ -80,9 +84,10 @@
<dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
<!-- testing and evaluation dependencies -->
- <dependency org="org.testng" name="testng" rev="5.14.1"/>
+ <dependency org="org.testng" name="testng" rev="6.8"/>
<dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
- <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT"/>
+ <dependency org="com.google.caliper" name="caliper" rev="0.5-rc1"/>
+ <dependency org="com.google.inject" name="guice" rev="3.0"/>
<!-- Contracts for Java and dependencies -->
<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
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