Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
c1263e841c
commit
4c147329a9
61
build.xml
61
build.xml
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@ -2,7 +2,9 @@
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<description>Compile and distribute the Sting toolkit</description>
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<property name="source.dir" value="java/src" />
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<property name="build.dir" value="build" />
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<property name="dist.dir" value="dist" />
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<property name="help.file" value="${build.dir}/help.properties" />
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<property name="single" value="*Test" />
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<property name="singleintegration" value="*IntegrationTest" />
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@ -24,6 +26,25 @@
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<property environment="env"/>
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<property name="target" value="${env.STING_BUILD_TYPE}" />
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<dirset id="source.files" dir="${source.dir}">
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<patternset>
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<include name="org/broadinstitute/sting/**"/>
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<exclude name="**/playground/**" unless="include.playground" />
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<exclude name="**/oneoffprojects/**" unless="include.oneoffs" />
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</patternset>
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</dirset>
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<patternset id="dependency.mask" includes="*.jar">
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<exclude name="junit*.jar" />
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<exclude name="bcel*.jar" />
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</patternset>
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<path id="runtime.dependencies">
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<fileset dir="lib">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<!-- ivy properties -->
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<property name="ivy.install.version" value="2.0.0"/>
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<property name="ivy.home" value="${user.home}/.ant"/>
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@ -60,17 +81,6 @@
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</or>
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</condition>
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<patternset id="dependency.mask" includes="*.jar">
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<exclude name="junit*.jar" />
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<exclude name="bcel*.jar" />
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</patternset>
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<path id="runtime.dependencies">
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<fileset dir="lib">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<!-- Create the build directory structure used by compile -->
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<mkdir dir="build"/>
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</target>
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@ -84,7 +94,17 @@
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</javac>
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</target>
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<target name="dist" depends="compile"
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<target name="extracthelp" depends="compile"
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description="Extract help key/value pair file from the JavaDoc tags.">
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<javadoc doclet="org.broadinstitute.sting.utils.doc.HelpExtractorDoclet"
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docletpath="build"
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classpathref="runtime.dependencies"
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additionalparam="-out ${help.file}">
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<packageset refid="source.files"/>
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</javadoc>
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</target>
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<target name="dist" depends="compile,extracthelp"
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description="generate the distribution">
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<mkdir dir="${dist.dir}"/>
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<delete>
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@ -101,6 +121,7 @@
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<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
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<fileset dir="build">
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<include name="help.properties" />
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<include name="**/gatk/**/*.class" />
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<include name="**/alignment/**/*.class"/>
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<include name="**/oneoffprojects/**/*.class" />
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@ -251,8 +272,8 @@
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<!-- where to put reports and tests-->
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<property name="report" value="build/report"/>
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<property name="test.classes" value="build/testclasses"/>
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<property name="report" value="${build.dir}/report"/>
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<property name="test.classes" value="${build.dir}/testclasses"/>
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<property name="test.output" value="${dist.dir}/test"/>
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<property name="test.sources" value="java/test"/>
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@ -261,7 +282,7 @@
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<mkdir dir="${report}"/>
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<echo message="Sting: Running test cases!"/>
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<junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
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<jvmarg value="-javaagent:build/TestAgent.jar"/>
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<jvmarg value="-javaagent:${build.dir}/TestAgent.jar"/>
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<formatter type="${testOutput}" usefile="${usefile}" />
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<classpath>
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<path refid="runtime.dependencies"/>
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@ -306,7 +327,7 @@
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<!-- this builds the instrumentation library we're going to use for test cases -->
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<target name="agent" description="build the agent">
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<echo message="Sting: Creating test agent!"/>
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<jar jarfile="build/TestAgent.jar">
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<jar jarfile="${build.dir}/TestAgent.jar">
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<fileset dir="build">
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<include name="**/TrivialInstrumenter.class" />
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</fileset>
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@ -322,13 +343,7 @@
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<mkdir dir="javadoc"/>
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<javadoc destdir="javadoc"
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classpathref="runtime.dependencies">
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<fileset dir="${source.dir}">
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<patternset>
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<include name="**/*.java"/>
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<exclude name="**/playground/**" unless="include.playground"/>
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<exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
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</patternset>
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</fileset>
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<packageset refid="source.files"/>
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</javadoc>
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</target>
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@ -0,0 +1,5 @@
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/**
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* Provides efficient access to GATK primary data sources
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* such as SAM files, fasta files, and reference-ordered data.
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*/
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package org.broadinstitute.sting.gatk.datasources;
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@ -1,11 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Provides efficient access to GATK primary data sources
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such as SAM files, fasta files, and reference-ordered data.
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</body>
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</html>
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@ -0,0 +1,6 @@
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/**
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* Provides a bridge from the block-at-a-time data access provided by
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* the datasource system to the locus / read-at-a-time data access
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* required by the traversal engine.
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*/
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package org.broadinstitute.sting.gatk.datasources.providers;
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@ -1,12 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Provides a bridge from the block-at-a-time data access provided by
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the datasource system to the locus / read-at-a-time data access
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required by the traversal engine.
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</body>
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</html>
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@ -0,0 +1,6 @@
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/**
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* Divides core input data into manageable blocks, each representing
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* a subsection of data that is small enough to be processed by a single
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* worker.
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*/
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package org.broadinstitute.sting.gatk.datasources.shards;
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@ -1,12 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Divides core input data into manageable blocks, each representing
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a subsection of data that is small enough to be processed by a single
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worker.
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</body>
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</html>
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/**
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* Retrieves core GATK data, given a shard which represents a contiguous
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* subsequence of core GATK data (reads, reference, or reference-ordered
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* data).
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*/
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package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
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@ -1,12 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Retrieves core GATK data, given a shard which represents a contiguous
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subsequence of core GATK data (reads, reference, or reference-ordered
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data).
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</body>
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</html>
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/**
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* Manages individual analyses by shattering data, pushing individual shards to the traversal engines, and gathering results and presenting them to the user.
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*/
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package org.broadinstitute.sting.gatk.executive;
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@ -1,10 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Manages individual analyses by shattering data, pushing individual shards to the traversal engines, and gathering results and presenting them to the user.
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</body>
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</html>
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@ -0,0 +1,4 @@
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/**
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* Provides a commonly used set of filters for determining which data should and should not be applied.
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*/
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package org.broadinstitute.sting.gatk.filters;
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@ -1,34 +0,0 @@
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<!--
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~ Copyright (c) 2009 The Broad Institute
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~ Permission is hereby granted, free of charge, to any person
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~ obtaining a copy of this software and associated documentation
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~ files (the "Software"), to deal in the Software without
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~ restriction, including without limitation the rights to use,
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~ copy, modify, merge, publish, distribute, sublicense, and/or sell
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~ copies of the Software, and to permit persons to whom the
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~ Software is furnished to do so, subject to the following
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~ conditions:
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~
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~ The above copyright notice and this permission notice shall be
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~ included in all copies or substantial portions of the Software.
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~
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~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
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"http://www.w3.org/TR/html4/loose.dtd">
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<html>
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<head>
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<title></title>
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</head>
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<body>
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Provides a commonly used set of filters for determining which data should and should not be applied.
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</body>
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</html>
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/**
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* Tools for iterating over different views of GATK data.
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*/
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package org.broadinstitute.sting.gatk.iterators;
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@ -1,10 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Tools for iterating over different views of GATK data.
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</body>
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</html>
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/**
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* Provides map/reduce application framework highly optimized for
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* analysis of sequencing data.
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*/
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package org.broadinstitute.sting.gatk;
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@ -1,11 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Provides map/reduce application framework highly optimized for
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analysis of sequencing data.
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</body>
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</html>
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/**
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* Reads and preprocesses the various types of data represented by the
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* GATK.
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*/
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package org.broadinstitute.sting.gatk.refdata;
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@ -1,10 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Reads and preprocesses the various types of data represented by the
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GATK.
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</body>
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</html>
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/**
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* Traverses over a shard of data, performing a mini-map/reduce on that
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* dataset.
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*/
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package org.broadinstitute.sting.gatk.traversals;
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@ -1,11 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Traverses over a shard of data, performing a mini-map/reduce on that
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dataset.
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</body>
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</html>
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/**
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* Runs the desired analysis on the smallest meaningful subset of the
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* dataset. Traditionally, the smallest subset is either an individual
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* locus or read.
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*/
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package org.broadinstitute.sting.gatk.walkers;
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@ -1,13 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<html>
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<head>
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</head>
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<body bgcolor="white">
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Runs the desired analysis on the smallest meaningful subset of the
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dataset. Traditionally, the smallest subset is either an individual
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locus or read.
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</body>
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</html>
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package org.broadinstitute.sting.utils.doc;
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import com.sun.javadoc.RootDoc;
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import com.sun.javadoc.PackageDoc;
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import com.sun.javadoc.ClassDoc;
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import java.util.HashSet;
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import java.util.Set;
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import java.util.Scanner;
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import java.io.PrintStream;
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import java.io.FileNotFoundException;
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/**
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* Extracts certain types of javadoc (specifically package and class descriptions) and makes them available
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* to applications at runtime.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class HelpExtractorDoclet {
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/**
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* Extracts the contents of certain types of javadoc and adds them to an XML file.
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* @param rootDoc The documentation root.
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* @return Whether the JavaDoc run succeeded.
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*/
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public static boolean start(RootDoc rootDoc) throws FileNotFoundException {
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PrintStream out = System.out;
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for(String[] options: rootDoc.options()) {
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if(options[0].equals("-out"))
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out = new PrintStream(options[1]);
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}
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// Cache packages as we see them, since there's no direct way to iterate over packages.
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Set<PackageDoc> packages = new HashSet<PackageDoc>();
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for(ClassDoc currentClass: rootDoc.classes()) {
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PackageDoc containingPackage = currentClass.containingPackage();
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packages.add(containingPackage);
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String className = containingPackage.name().length() > 0 ?
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String.format("%s.%s",containingPackage.name(),currentClass.name()) :
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String.format("%s",currentClass.name());
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String commentText = formatText(currentClass.commentText());
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if(commentText.length() > 0)
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out.printf("%s=%s%n",className,commentText);
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}
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for(PackageDoc currentPackage: packages) {
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String commentText = formatText(currentPackage.commentText());
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if(commentText.length() > 0)
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out.printf("%s=%s%n",currentPackage.name(),commentText);
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}
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return true;
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}
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/**
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* Validate the given options against
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* @param option
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* @return
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*/
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public static int optionLength(String option) {
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if(option.equals("-out")) {
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return 2;
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}
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return 0;
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}
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/**
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* Format text for consumption by the properties file.
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* @param text Text to format.
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* @return Formatted text; string trimmed, newlines removed.
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*/
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private static String formatText(String text) {
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Scanner scanner = new Scanner(text);
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StringBuilder output = new StringBuilder();
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while(scanner.hasNextLine()) {
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if(output.length() > 0)
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output.append(' ');
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output.append(scanner.nextLine().trim());
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}
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return output.toString();
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}
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}
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