Examples of GenotypeCalculationArgumentCollection

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

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public class GeneralPloidyFailOverAFCalculatorProviderUnitTest {

    @Test(dataProvider="nonThreadSafeConstructorsData")
    public void testNonThreadSafeConstructors(final int ploidy, final int maxAltAlleles) {
        final GenotypeCalculationArgumentCollection args = new GenotypeCalculationArgumentCollection();
        args.MAX_ALTERNATE_ALLELES = maxAltAlleles;
        args.samplePloidy = ploidy;

        final GeneralPloidyFailOverAFCalculatorProvider provider = new GeneralPloidyFailOverAFCalculatorProvider(args,null);

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

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        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;
        genotypeArgs.MAX_ALTERNATE_ALLELES = maxAltAlleles;
        final AFCalculatorProvider provider = GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit,genotypeArgs,null);
        final Hashtable<Thread,AFCalculator> perThreadProvider = new Hashtable(cpuThreadCount * dataThreadCount);
        final List<Thread> threads = new ArrayList<>();
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Examples of org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection

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*/
public class FixedAFCalculatorProviderUnitTest {

    @Test(dataProvider="nonThreadSafeConstructorsData")
    public void testNonThreadSafeConstructors(final int ploidy, final int maxAltAlleles, final AFCalculatorImplementation preferred) {
        final GenotypeCalculationArgumentCollection args = new GenotypeCalculationArgumentCollection();
        args.MAX_ALTERNATE_ALLELES = maxAltAlleles;
        args.samplePloidy = ploidy;
        final StandardCallerArgumentCollection callerArgs = new StandardCallerArgumentCollection();
        if (preferred != null ) callerArgs.requestedAlleleFrequencyCalculationModel = preferred;
        callerArgs.genotypeArgs = args;
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Examples of org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection

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        gatkArguments.numberOfCPUThreadsPerDataThread =cpuThreadCount;
        gatkArguments.numberOfDataThreads = dataThreadCount;
        toolkit.setArguments(gatkArguments);
        final StandardCallerArgumentCollection callerArgs = new StandardCallerArgumentCollection();
        if (impl != null) callerArgs.requestedAlleleFrequencyCalculationModel = impl;
        final GenotypeCalculationArgumentCollection genotypeArgs = new GenotypeCalculationArgumentCollection();
        callerArgs.genotypeArgs = genotypeArgs;
        genotypeArgs.samplePloidy = ploidy;
        genotypeArgs.MAX_ALTERNATE_ALLELES = maxAltAlleles;
        final AFCalculatorProvider provider = FixedAFCalculatorProvider.createThreadSafeProvider(toolkit,callerArgs,null);
        final Hashtable<Thread,AFCalculator> perThreadProvider = new Hashtable(cpuThreadCount * dataThreadCount);
 
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