Package org.broadinstitute.gatk.engine.arguments

Examples of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

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    public static AFCalculatorProvider createThreadSafeProvider(final GenomeAnalysisEngine toolkit,
                                                                final GenotypeCalculationArgumentCollection genotypeArgs,
                                                                final Logger logger) {
        if (genotypeArgs == null)
            throw new IllegalArgumentException("genotype arguments object cannot be null");
        final GATKArgumentCollection arguments = toolkit.getArguments();
        final boolean isMultithread = arguments.numberOfDataThreads > 1 || arguments.numberOfCPUThreadsPerDataThread > 1;
        return isMultithread ? new ConcurrentAFCalculatorProvider() {
            @Override
            protected AFCalculatorProvider createProvider() {
                return new GeneralPloidyFailOverAFCalculatorProvider(genotypeArgs,logger);
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     * @return never {@code null}
     */
    public static AFCalculatorProvider createThreadSafeProvider(final GenomeAnalysisEngine toolkit,
                                                                final StandardCallerArgumentCollection config,
                                                                final Logger logger) {
        final GATKArgumentCollection arguments = toolkit.getArguments();
        final boolean isMultithread = arguments.numberOfCPUThreadsPerDataThread > 1 || arguments.numberOfDataThreads > 1;
        return !isMultithread
                ? new FixedAFCalculatorProvider(config,logger,false) :
                new ConcurrentAFCalculatorProvider() {
                    @Override
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     */
    @SuppressWarnings("unused")
    public static AFCalculatorProvider createThreadSafeProvider(final GenomeAnalysisEngine toolkit,
                                                                  final StandardCallerArgumentCollection config,
                                                                  final Logger logger, final boolean verifyRequests) {
        final GATKArgumentCollection arguments = toolkit.getArguments();
        final boolean isMultithread = arguments.numberOfCPUThreadsPerDataThread > 1 || arguments.numberOfDataThreads > 1;
        return !isMultithread
                ? new FixedAFCalculatorProvider(config,logger,verifyRequests) :
                new ConcurrentAFCalculatorProvider() {
                    @Override
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    }

    @Test(dataProvider="threadSafeFactoryData")
    public void testThreadSafeConstructors(final int ploidy, final int maxAltAlleles, final int cpuThreadCount, final int dataThreadCount) {
        final GenomeAnalysisEngine toolkit = new GenomeAnalysisEngine();
        final GATKArgumentCollection gatkArguments = new GATKArgumentCollection();
        gatkArguments.numberOfCPUThreadsPerDataThread =cpuThreadCount;
        gatkArguments.numberOfDataThreads = dataThreadCount;
        toolkit.setArguments(gatkArguments);
        final GenotypeCalculationArgumentCollection genotypeArgs = new GenotypeCalculationArgumentCollection();
        genotypeArgs.samplePloidy = ploidy;
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    }

    @Test(dataProvider="threadSafeFactoryData")
    public void testThreadSafeConstructors(final int ploidy, final int maxAltAlleles, final AFCalculatorImplementation impl, final int cpuThreadCount, final int dataThreadCount) {
        final GenomeAnalysisEngine toolkit = new GenomeAnalysisEngine();
        final GATKArgumentCollection gatkArguments = new GATKArgumentCollection();
        gatkArguments.numberOfCPUThreadsPerDataThread =cpuThreadCount;
        gatkArguments.numberOfDataThreads = dataThreadCount;
        toolkit.setArguments(gatkArguments);
        final StandardCallerArgumentCollection callerArgs = new StandardCallerArgumentCollection();
        if (impl != null) callerArgs.requestedAlleleFrequencyCalculationModel = impl;
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    private UnifiedGenotypingEngine ugEngine;

    @BeforeClass
    public void setUp() throws Exception {
        final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
        engine.setArguments(new GATKArgumentCollection());

        final UnifiedArgumentCollection args = new UnifiedArgumentCollection();
        final SampleList fakeSamples = SampleListUtils.singletonList("fake");

        ugEngine = new UnifiedGenotypingEngine(args,fakeSamples,engine.getGenomeLocParser(),
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    public void timeWalkerPerformance(final int reps) {
        for(int i = 0; i < reps; i++) {
            GenomeAnalysisEngine engine = new GenomeAnalysisEngine();

            // Establish the argument collection
            GATKArgumentCollection argCollection = new GATKArgumentCollection();
            argCollection.referenceFile = new File(referenceFile);
            argCollection.samFiles = Collections.singletonList(inputFile.getAbsolutePath());

            engine.setArguments(argCollection);
            // Bugs in the engine mean that this has to be set twice.
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    public void testEmptySamFileListHandling() throws Exception {
        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
        testEngine.setWalker(new CountReads()); //generalizable to any walker requiring reads

        //supply command line args so validateSuppliedReads() knows whether reads were passed in
        GATKArgumentCollection testArgs = new GATKArgumentCollection();
        testArgs.samFiles.add("empty.list");
        testEngine.setArguments(testArgs);

        //represents the empty list of samFiles read in from empty.list by CommandLineExecutable
        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
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        //HeapSizeMonitor monitor = new HeapSizeMonitor();
        //monitor.start();
        setStartTime(new java.util.Date());

        final GATKArgumentCollection args = this.getArguments();

        // validate our parameters
        if (args == null) {
            throw new ReviewedGATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
        }
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        return MicroScheduler.create(this,walker,this.getReadsDataSource(),this.getReferenceDataSource().getReference(),this.getRodDataSources(),threadAllocation);
    }

    protected DownsamplingMethod getDownsamplingMethod() {
        GATKArgumentCollection argCollection = this.getArguments();

        DownsamplingMethod commandLineMethod = argCollection.getDownsamplingMethod();
        DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker);

        DownsamplingMethod method = commandLineMethod != null ? commandLineMethod : walkerMethod;
        method.checkCompatibilityWithWalker(walker);
        return method;
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Related Classes of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

  • org.broadinstitute.gatk.engine.datasources.reads.GATKWalkerBenchmark
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngineUnitTest
  • org.broadinstitute.gatk.engine.phonehome.GATKRunReportUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProviderUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyFailOverAFCalculatorProvider
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyFailOverAFCalculatorProviderUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyperEngineUnitTest
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