Package org.broadinstitute.gatk.engine.arguments

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

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    @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;
        final FixedAFCalculatorProvider providerCallerArgs = new FixedAFCalculatorProvider(callerArgs,null,true);
        final FixedAFCalculatorProvider providerGenotypingArgs = new FixedAFCalculatorProvider(args,null,true);
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        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;
        final GenotypeCalculationArgumentCollection genotypeArgs = new GenotypeCalculationArgumentCollection();
        callerArgs.genotypeArgs = genotypeArgs;
        genotypeArgs.samplePloidy = ploidy;
        genotypeArgs.MAX_ALTERNATE_ALLELES = maxAltAlleles;
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           }
    }

    @Test(dataProvider="collectionClassPairs")
    public void testCloneTo(final Class<? extends StandardCallerArgumentCollection> fromClass, final Class<? extends StandardCallerArgumentCollection> toClass) {
        final StandardCallerArgumentCollection fromObject;
        try {
            fromObject = randomArgumentCollection(fromClass);
        } catch (final IllegalAccessException e) {
            throw new SkipException("cannot create a random configuration");
        } catch (final InstantiationException e) {
            throw new SkipException("cannot create a random configuration");
        }

        final StandardCallerArgumentCollection toObject = fromObject.cloneTo(toClass);
        Assert.assertNotNull(toObject);
        Assert.assertEquals(toClass,toObject.getClass());
        for (final Field field : fromClass.getFields())
            if (!field.getDeclaringClass().isAssignableFrom(toClass))
                continue;
            else if (Modifier.isPrivate(field.getModifiers()))
                continue;
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Related Classes of org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection

  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProviderUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollectionUnitTest
  • java.lang.reflect.Method
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