Added new utility files used by maven build, including the ant-bridge script.
This commit is contained in:
Khalid Shakir
David Roazen
parent
88150e0166
commit
d1a689af33
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@ -0,0 +1,158 @@
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#!/bin/sh
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mvn_args="test-compile"
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mvn_properties=
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mvn_clean=
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unknown_args=
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property_regex='-D(.*)=(.*)'
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unit_test_regex='.*UnitTest'
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post_script=
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for arg in "${@}" ; do
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if [ "${arg}" = "clean" ] ; then
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mvn_clean="clean"
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mvn_args=
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elif [[ "${arg}" =~ ${property_regex} ]] ; then
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property_name=${BASH_REMATCH[1]}
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property_value=${BASH_REMATCH[2]}
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if [ "${property_name}" = "single" ] ; then
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test_property="test"
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test_disabled="it.test"
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if [[ ! "${property_value}" =~ ${unit_test_regex} ]] ; then
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test_property="it.test"
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test_disabled="test"
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fi
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mvn_properties="${mvn_properties} -D${test_disabled}=disabled -D${test_property}=${property_value}"
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elif [ "${property_name}" = "test.debug.port" ] ; then
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mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
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elif [ "${property_name}" = "test.default.maxmemory" ] ; then
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mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
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else
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unknown_args="${unknown_args} \"${arg}\""
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fi
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else
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if [ "${arg}" != "dist" -a "${mvn_args}" != "test-compile" ]; then
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echo "Sorry, this script does not currently support mixing targets." >&2
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exit 1
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elif [ "${arg}" = "dist" ] ; then
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mvn_args="test-compile"
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elif [ "${arg}" = "gatkdocs" ] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} -Ddisable.queue && mvn site -Dmaven.repo.local=${local_repo} -Ddisable.queue"
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elif [ "${arg}" = "package.gatk.full" ] ; then
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mvn_args="package '-P!private,!queue'"
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elif [ "${arg}" = "package.gatk.all" ] ; then
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mvn_args="package '-P!queue'"
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elif [ "${arg}" = "package.queue.full" ] ; then
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mvn_args="package '-P!private'"
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elif [ "${arg}" = "package.queue.all" ] ; then
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mvn_args="package"
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elif [ "${arg}" = "release.gatk.full" ] ; then
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mvn_args="package '-P!private,!queue'"
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post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
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elif [ "${arg}" = "release.queue.full" ] ; then
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mvn_args="package '-P!private'"
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post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
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elif [ "${arg}" = "build-picard-private" ] ; then
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mvn_args="mvn install -f private/picard-maven/pom.xml"
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# TODO: clover support
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# see ant and maven docs for clover:
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# https://confluence.atlassian.com/display/CLOVER/1.+QuickStart+Guide
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# https://confluence.atlassian.com/display/CLOVER/Clover-for-Maven+2+and+3+User%27s+Guide
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#
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#elif [ "${arg}" = "clover.report" ] ; then
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# mvn_args=...
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#
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#elif [ "${arg}" = "with.clover" ] ; then
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# mvn_args=...
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# TODO: This runs *all* commit tests, including the few on Queue.
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elif [ "${arg}" = "gatkfull.binary.release.tests" ] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
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mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
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mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
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mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
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mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
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# TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
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elif [ "${arg}" = "queuefull.binary.release.tests" ] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
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mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
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mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
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mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
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mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
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mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
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elif [ "${arg}" = "committests" ] ; then
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mvn_args="verify -Dsting.committests.skipped=false"
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elif [ "${arg}" = "test" ] ; then
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mvn_args="test -Dsting.unittests.skipped=false"
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elif [ "${arg}" = "unittest" ] ; then
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mvn_args="test -Dsting.unittests.skipped=false"
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elif [ "${arg}" = "integrationtest" ] ; then
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mvn_args="verify -Dsting.integrationtests.skipped=false"
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elif [ "${arg}" = "largescaletest" ] ; then
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mvn_args="verify -Dsting.largescaletests.skipped=false"
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elif [ "${arg}" = "pipelinetest" ] ; then
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mvn_args="verify -Dsting.pipelinetests.skipped=false"
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elif [ "${arg}" = "pipelinetestrun" ] ; then
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mvn_args="verify -Dsting.pipelinetests.skipped=false -Dsting.pipelinetests.run=true"
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elif [ "${arg}" = "fasttest" ] ; then
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mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true"
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else
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unknown_args="${unknown_args} \"${arg}\""
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fi
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fi
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done
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mvn_cmd=
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if [ "${mvn_clean}" != "" ]; then
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if [ "${mvn_args}" != "" ]; then
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mvn_cmd="mvn ${mvn_clean} && mvn ${mvn_args}"
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else
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mvn_cmd="mvn ${mvn_clean}"
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fi
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else
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mvn_cmd="mvn ${mvn_args}"
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fi
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if [ "${unknown_args}" != "" ]; then
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echo "Unrecognized arguments:${unknown_args}" >&2
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else
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echo "Equivalent maven command"
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echo "${mvn_cmd}${mvn_properties}${post_script}"
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sh -c "${mvn_cmd}${mvn_properties}${post_script}"
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fi
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@ -0,0 +1,56 @@
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.mycompany.app;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import java.io.PrintStream;
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/**
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* An example walker that looks surprisingly like CountLoci.
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*/
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public class MyExampleWalker extends LocusWalker<Integer, Long> {
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@Output
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PrintStream out;
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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return 1;
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}
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public Long reduceInit() { return 0l; }
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public Long reduce(Integer value, Long sum) {
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return value + sum;
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}
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public void onTraversalDone( Long c ) {
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out.println(c);
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}
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}
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@ -0,0 +1,54 @@
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.mycompany.app;
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import org.broadinstitute.sting.WalkerTest;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.util.Collections;
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import java.util.MissingResourceException;
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/**
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* NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad.
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*/
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public class MyExampleWalkerIntegrationTest extends WalkerTest {
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@Test
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public void testMyExampleWalker() throws URISyntaxException {
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String gatk_args = String.format("-T MyExampleWalker -I %s -R %s", getResource("/exampleBAM.bam"), getResource("/exampleFASTA.fasta"));
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WalkerTestSpec spec = new WalkerTestSpec(gatk_args, Collections.<String>emptyList());
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executeTest("Testing count on the example bam", spec);
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}
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private File getResource(String path) throws URISyntaxException {
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URL resourceUrl = getClass().getResource(path);
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if (resourceUrl == null)
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throw new MissingResourceException("Resource not found: " + path, getClass().getSimpleName(), path);
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return new File(resourceUrl.toURI());
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}
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}
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@ -0,0 +1,41 @@
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.mycompany.app;
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import org.broadinstitute.sting.BaseTest;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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/**
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* NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad.
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*/
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public class MyExampleWalkerUnitTest extends BaseTest {
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@Test
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public void testMyExampleWalker() {
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MyExampleWalker walker = new MyExampleWalker();
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Assert.assertEquals((long)walker.reduce(1, 1L), 2L);
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}
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}
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@ -0,0 +1,37 @@
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<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
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<id>example-resources</id>
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<formats>
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<format>tar.bz2</format>
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</formats>
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<includeBaseDirectory>false</includeBaseDirectory>
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<fileSets>
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<fileSet>
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<directory>${project.build.sourceDirectory}/org/broadinstitute/sting/gatk/walkers/qc</directory>
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<outputDirectory>.</outputDirectory>
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<includes>
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<include>Pileup.java</include>
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<include>CountLoci.java</include>
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<include>CountReads.java</include>
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<include>CheckPileup.java</include>
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</includes>
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</fileSet>
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<fileSet>
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<directory>${project.build.sourceDirectory}/org/broadinstitute/sting/gatk/walkers/readutils</directory>
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<outputDirectory>.</outputDirectory>
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<includes>
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<include>PrintReads.java</include>
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</includes>
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</fileSet>
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<fileSet>
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<directory>src/test/resources</directory>
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<outputDirectory>.</outputDirectory>
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<includes>
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<include>exampleBAM.bam</include>
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<include>exampleBAM.bam.bai</include>
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<include>exampleFASTA.fasta</include>
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<include>exampleFASTA.fasta.fai</include>
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<include>exampleFASTA.dict</include>
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</includes>
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</fileSet>
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</fileSets>
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</assembly>
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@ -0,0 +1,22 @@
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<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
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<id>binary-dist</id>
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<formats>
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<format>tar.bz2</format>
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</formats>
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<includeBaseDirectory>false</includeBaseDirectory>
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<dependencySets>
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<dependencySet>
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<includes>
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<include>org.broadinstitute.sting:gatk-package</include>
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</includes>
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<outputFileNameMapping>${sting.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
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</dependencySet>
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<dependencySet>
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<outputDirectory>resources</outputDirectory>
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<unpack>true</unpack>
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<includes>
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<include>org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources</include>
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</includes>
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</dependencySet>
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</dependencySets>
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</assembly>
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@ -0,0 +1,13 @@
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<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
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<id>gsalib</id>
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<formats>
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<format>tar.gz</format>
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</formats>
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<includeBaseDirectory>false</includeBaseDirectory>
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<fileSets>
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<fileSet>
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<outputDirectory>gsalib</outputDirectory>
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<directory>src/R</directory>
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</fileSet>
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</fileSets>
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</assembly>
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<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
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<id>example-resources</id>
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<formats>
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<format>tar.bz2</format>
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</formats>
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<includeBaseDirectory>false</includeBaseDirectory>
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<fileSets>
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<fileSet>
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<directory>src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples</directory>
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<outputDirectory>.</outputDirectory>
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<includes>
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<include>ExampleCountReads.scala</include>
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<include>ExampleCountLoci.scala</include>
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<include>ExampleUnifiedGenotyper.scala</include>
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<include>ExampleReadFilter.scala</include>
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<include>ExampleCustomWalker.scala</include>
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</includes>
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</fileSet>
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</fileSets>
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</assembly>
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@ -0,0 +1,23 @@
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<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
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<id>binary-dist</id>
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<formats>
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<format>tar.bz2</format>
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</formats>
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<includeBaseDirectory>false</includeBaseDirectory>
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<dependencySets>
|
||||
<dependencySet>
|
||||
<includes>
|
||||
<include>org.broadinstitute.sting:queue-package</include>
|
||||
</includes>
|
||||
<outputFileNameMapping>${sting.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
|
||||
</dependencySet>
|
||||
<dependencySet>
|
||||
<outputDirectory>resources</outputDirectory>
|
||||
<unpack>true</unpack>
|
||||
<includes>
|
||||
<include>org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources</include>
|
||||
<include>org.broadinstitute.sting:queue-framework:tar.bz2:example-resources</include>
|
||||
</includes>
|
||||
</dependencySet>
|
||||
</dependencySets>
|
||||
</assembly>
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
# Root logger option
|
||||
log4j.rootLogger=INFO, stdout
|
||||
|
||||
# Direct log messages to stdout
|
||||
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
|
||||
log4j.appender.stdout.Target=System.out
|
||||
log4j.appender.stdout.layout=org.apache.log4j.SimpleLayout
|
||||
Loading…
Reference in New Issue