1. Added support for building the PairHMM vector library into build.xml.
The library is compiled using makefile and copied into the directory: build/java/classes/org/broadinstitute/sting/utils/pairhmm/ 2. Bundled the library into StingUtils.jar. Unpacked and loaded at runtime without the need to set java.library.path Caveats: Platform independence has probably been thrown out of the window. Assumptions: a. make command exists at /usr/bin/make b. rsync command exists at /usr/bin/rsync c. icc is in the PATH of the user
This commit is contained in:
Karthik Gururaj
parent
7815c30df8
commit
dc44b64ad8
125
build.xml
125
build.xml
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@ -64,6 +64,7 @@
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<property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
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<property name="R.protected.scripts.dir" value="${protected.dir}/R/scripts" />
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<property name="R.public.src.dir" value="${public.dir}/R/src" />
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<property name="vector.pairhmm.library.source.dir" value="${public.dir}/c++/VectorPairHMM" />
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<!-- Build directories -->
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<property name="java.classes" value="${build.dir}/java/classes" />
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@ -270,21 +271,21 @@
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<mkdir dir="${lib.dir}"/>
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<mkdir dir="${ivy.jar.dir}"/>
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<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
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<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
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<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${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}/${maven-ant-tasks.jar.file}"/>
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<!-- End network lines -->
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@ -601,14 +602,14 @@
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<path id="doclet.classpath">
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<path refid="external.dependencies" />
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<pathelement location="${java.classes}" />
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<pathelement location="${clover.jar}" />
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<pathelement location="${clover.jar}" />
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</path>
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<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
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docletpathref="doclet.classpath"
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classpathref="external.dependencies"
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classpath="${java.classes}"
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maxmemory="2g"
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maxmemory="2g"
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additionalparam="-build-timestamp "${build.timestamp}" -absolute-version ${build.version} -out ${basedir}/${resource.path} -quiet">
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<sourcefiles>
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<union>
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@ -648,9 +649,23 @@
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</copy>
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</target>
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<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
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<target name="build.vector.pairhmm.library">
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<exec dir="${vector.pairhmm.library.source.dir}" executable="/usr/bin/make">
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</exec>
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</target>
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<target name="copy.vector.pairhmm.library" depends="build.vector.pairhmm.library">
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<exec executable="/usr/bin/rsync">
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<arg value="-a"/>
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<arg value="${vector.pairhmm.library.source.dir}/libVectorLoglessPairHMM.so"/>
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<arg value="${java.classes}/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so"/>
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</exec>
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</target>
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<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage, copy.vector.pairhmm.library">
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<jar jarfile="${dist.dir}/StingUtils.jar">
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<fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
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<fileset dir="${java.classes}" includes="**/sting/utils/**/*.so"/>
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<fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
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<fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
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<fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
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@ -682,9 +697,9 @@
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<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
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<include name="net/sf/picard/reference/FastaSequenceFile.class"/>
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</fileset>
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<fileset dir="${java.private.source.dir}">
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<fileset dir="${java.private.source.dir}">
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<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
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</fileset>
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</fileset>
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</jar>
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</target>
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@ -693,7 +708,7 @@
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<path refid="gatk.resources"/>
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<fileset dir="${java.contracts.dir}" />
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<fileset dir="${java.classes}">
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<include name="${resource.file}" />
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<include name="${resource.file}" />
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<include name="**/sting/gatk/**/*.class" />
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<include name="**/sting/alignment/**/*.class"/>
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</fileset>
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@ -815,7 +830,7 @@
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docletpathref="doclet.classpath"
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classpathref="external.dependencies"
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classpath="${java.classes}"
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maxmemory="2g"
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maxmemory="2g"
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additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp "${build.timestamp}" -absolute-version ${build.version} -quiet"> <!-- -test to only do DocumentationTest walker -->
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<sourcefiles>
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<fileset refid="java.source.files"/>
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@ -974,10 +989,10 @@
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<!-- Build out a classpath -->
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<pathconvert property="required.picard.jars" pathsep=":">
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<fileset dir="${basedir}">
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<include name="${staging.dir}" />
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<include name="${lib.dir}/picard-*.*.*.jar" />
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<include name="${lib.dir}/sam-*.jar" />
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</fileset>
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<include name="${staging.dir}" />
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<include name="${lib.dir}/picard-*.*.*.jar" />
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<include name="${lib.dir}/sam-*.jar" />
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</fileset>
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</pathconvert>
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<echo message="required.picard.jars=${required.picard.jars}" />
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@ -990,7 +1005,7 @@
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<mkdir dir="${package.output.dir}" />
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<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
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<ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
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<property name="additional.jars" value="${required.picard.jars}" />
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<property name="additional.jars" value="${required.picard.jars}" />
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</ant>
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</target>
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@ -1149,31 +1164,31 @@
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<target name="clover.report">
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<clover-report coverageCacheSize="nocache">
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<current outfile="clover_html" title="GATK clover report" showUniqueCoverage="false" numThreads="4">
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<format type="html" filter="catch,static,property"/>
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<fileset dir="public">
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<patternset id="clover.excludes">
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<exclude name="**/*UnitTest.java"/>
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<exclude name="**/*TestProvider*.java"/>
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<exclude name="**/*PerformanceTest.java"/>
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<exclude name="**/*Benchmark.java"/>
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<exclude name="**/*LargeScaleTest.java"/>
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<exclude name="**/*IntegrationTest.java"/>
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<exclude name="**/jna/**/*.java"/>
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<exclude name="**/queue/extensions/**/*.java"/>
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<exclude name="**/sting/utils/help/*.java"/>
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<exclude name="**/sting/tools/*.java"/>
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<exclude name="**/datasources/reads/utilities/*.java"/>
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<exclude name="**/sting/alignment/**/*.java"/>
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<exclude name="**/examples/**/*.java"/>
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</patternset>
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</fileset>
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<fileset dir="private">
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<patternset refid="clover.excludes" />
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</fileset>
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<fileset dir="protected">
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<patternset refid="clover.excludes" />
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</fileset>
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</current>
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<format type="html" filter="catch,static,property"/>
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<fileset dir="public">
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<patternset id="clover.excludes">
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<exclude name="**/*UnitTest.java"/>
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<exclude name="**/*TestProvider*.java"/>
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<exclude name="**/*PerformanceTest.java"/>
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<exclude name="**/*Benchmark.java"/>
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<exclude name="**/*LargeScaleTest.java"/>
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<exclude name="**/*IntegrationTest.java"/>
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<exclude name="**/jna/**/*.java"/>
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<exclude name="**/queue/extensions/**/*.java"/>
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<exclude name="**/sting/utils/help/*.java"/>
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<exclude name="**/sting/tools/*.java"/>
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<exclude name="**/datasources/reads/utilities/*.java"/>
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<exclude name="**/sting/alignment/**/*.java"/>
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<exclude name="**/examples/**/*.java"/>
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</patternset>
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</fileset>
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<fileset dir="private">
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<patternset refid="clover.excludes" />
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</fileset>
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<fileset dir="protected">
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<patternset refid="clover.excludes" />
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</fileset>
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</current>
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</clover-report>
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</target>
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@ -1220,7 +1235,7 @@
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<target name="test.scala.compile" depends="test.java.compile,scala.compile" if="include.scala">
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<echo message="Scala: Compiling test cases!"/>
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<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes" addparams="-feature">
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<src refid="scala.test.source.path" />
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<src refid="scala.test.source.path" />
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<classpath>
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<path refid="build.results"/>
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<pathelement location="${java.test.classes}"/>
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@ -1266,13 +1281,13 @@
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<echo message="Sting: Running @{testtype} test cases!"/>
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<echo message="Test Memory : ${test.maxmemory}" />
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<!-- no test is allowed to run for more than 10 hours -->
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<!-- no test is allowed to run for more than 10 hours -->
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<taskdef resource="testngtasks" classpath="${testng.jar}"/>
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<testng outputDir="@{outputdir}"
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classpathref="${testng.classpath}"
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haltOnFailure="false" failureProperty="test.failure"
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verbose="2"
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timeout="36000000"
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timeout="36000000"
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workingDir="${basedir}"
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useDefaultListeners="false"
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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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@ -1308,7 +1323,7 @@
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<report format="noframes" todir="@{outputdir}"/>
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</junitreport>
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<!-- copy the report to our private_html directory for easy viewing in a broswer -->
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<!-- copy the report to our private_html directory for easy viewing in a broswer -->
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<mkdir dir="${iwww.report.dir}/@{testtype}"/>
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<copy todir="${iwww.report.dir}/@{testtype}" verbose="false">
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<fileset dir="@{outputdir}"/>
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@ -1442,7 +1457,7 @@
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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" description="Quickly run a single test">
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<property name="test.maxmemory" value="${test.default.maxmemory}"/>
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<property name="test.maxmemory" value="${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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@ -59,6 +59,15 @@ import java.util.List;
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import java.util.Map;
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import java.util.HashMap;
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//For loading library from jar
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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/**
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* Created with IntelliJ IDEA.
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@ -111,7 +120,28 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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synchronized(isVectorLoglessPairHMMLibraryLoaded) {
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//Load the library and initialize the FieldIDs
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if(!isVectorLoglessPairHMMLibraryLoaded) {
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System.loadLibrary("VectorLoglessPairHMM");
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try
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{
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//Try loading from Java's library path first
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//Useful if someone builds his/her own library and wants to override the bundled
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//implementation without modifying the Java code
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System.loadLibrary("VectorLoglessPairHMM");
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}
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catch(UnsatisfiedLinkError ule)
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{
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//Could not load from Java's library path - try unpacking from jar
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try
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{
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logger.info("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar");
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loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so");
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}
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catch(IOException ioe)
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{
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//Throw the UnsatisfiedLinkError to make it clear to the user what failed
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throw ule;
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}
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}
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isVectorLoglessPairHMMLibraryLoaded = true;
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jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll); //need to do this only once
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}
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@ -229,4 +259,75 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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super.close();
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jniClose();
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}
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//Copied from http://frommyplayground.com/how-to-load-native-jni-library-from-jar
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/**
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* Loads library from current JAR archive
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*
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* The file from JAR is copied into system temporary directory and then loaded. The temporary file is deleted after exiting.
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* Method uses String as filename because the pathname is "abstract", not system-dependent.
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*
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* @param filename The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext
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* @throws IOException If temporary file creation or read/write operation fails
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* @throws IllegalArgumentException If source file (param path) does not exist
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* @throws IllegalArgumentException If the path is not absolute or if the filename is shorter than three characters (restriction of {@see File#createTempFile(java.lang.String, java.lang.String)}).
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*/
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public static void loadLibraryFromJar(String path) throws IOException {
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if (!path.startsWith("/")) {
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throw new IllegalArgumentException("The path to be absolute (start with '/').");
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}
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// Obtain filename from path
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String[] parts = path.split("/");
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String filename = (parts.length > 1) ? parts[parts.length - 1] : null;
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// Split filename to prexif and suffix (extension)
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String prefix = "";
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String suffix = null;
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if (filename != null) {
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parts = filename.split("\\.", 2);
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prefix = parts[0];
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suffix = (parts.length > 1) ? "."+parts[parts.length - 1] : null; // Thanks, davs! :-)
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}
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// Check if the filename is okay
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if (filename == null || prefix.length() < 3) {
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throw new IllegalArgumentException("The filename has to be at least 3 characters long.");
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}
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// Prepare temporary file
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File temp = File.createTempFile(prefix, suffix);
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//System.out.println("Temp lib file "+temp.getAbsolutePath());
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temp.deleteOnExit();
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if (!temp.exists()) {
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throw new FileNotFoundException("File " + temp.getAbsolutePath() + " does not exist.");
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}
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// Prepare buffer for data copying
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byte[] buffer = new byte[1024];
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int readBytes;
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// Open and check input stream
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InputStream is = VectorLoglessPairHMM.class.getResourceAsStream(path);
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if (is == null) {
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throw new FileNotFoundException("File " + path + " was not found inside JAR.");
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}
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// Open output stream and copy data between source file in JAR and the temporary file
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OutputStream os = new FileOutputStream(temp);
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try {
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while ((readBytes = is.read(buffer)) != -1) {
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os.write(buffer, 0, readBytes);
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}
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} finally {
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// If read/write fails, close streams safely before throwing an exception
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os.close();
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is.close();
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}
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// Finally, load the library
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System.load(temp.getAbsolutePath());
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}
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}
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