Package org.broadinstitute.gatk.tools.walkers.bqsr

Examples of org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection

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        ReadCovariates.clearKeysCache();
    }

    @Test(enabled = false)
    public void testCovariateGeneration() {
        final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
        final String RGID = "id";

        ReadGroupCovariate rgCov = new ReadGroupCovariate();
        QualityScoreCovariate qsCov = new QualityScoreCovariate();
        ContextCovariate coCov = new ContextCovariate();
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    ContextCovariate covariate;
    RecalibrationArgumentCollection RAC;

    @BeforeClass
    public void init() {
        RAC = new RecalibrationArgumentCollection();
        covariate = new ContextCovariate();
        covariate.initialize(RAC);
    }
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            quals.add((byte) i);
            counts.add(1L);
        }

        final QuantizationInfo quantizationInfo = new QuantizationInfo(quals, counts);
        final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();

        quantizationInfo.noQuantization();
        final List<Covariate> requiredCovariates = new LinkedList<Covariate>();
        final List<Covariate> optionalCovariates = new LinkedList<Covariate>();
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    ReadGroupCovariate covariate;
    RecalibrationArgumentCollection RAC;

    @BeforeClass
    public void init() {
        RAC = new RecalibrationArgumentCollection();
        covariate = new ReadGroupCovariate();
        covariate.initialize(RAC);
    }
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        runTest(rg, expected, covariate);
    }

    @Test(enabled = true)
    public void testForceReadgroup() {
        final RecalibrationArgumentCollection forcedRAC = new RecalibrationArgumentCollection();
        forcedRAC.FORCE_READGROUP = "FOO";
        final ReadGroupCovariate forcedCovariate = new ReadGroupCovariate();
        forcedCovariate.initialize(forcedRAC);

        final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("NOT_FOO");
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* Time: 1:06 PM
* To change this template use File | Settings | File Templates.
*/
public class RecalibrationTestUtils {
    public static Covariate[] makeInitializedStandardCovariates() {
        final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
        final Covariate[] covariates = new Covariate[4];
        covariates[0] = new ReadGroupCovariate();
        covariates[1] = new QualityScoreCovariate();
        covariates[2] = new ContextCovariate();
        covariates[3] = new CycleCovariate();
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    @BeforeClass
    public void init() {
        RAC = new RecalibrationArgumentCollection();
        rlCovariate = new RepeatLengthCovariate();
        ruCovariate = new RepeatUnitCovariate();
        rurlCovariate = new RepeatUnitAndLengthCovariate();
        rlCovariate.initialize(RAC);
        ruCovariate.initialize(RAC);
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    CycleCovariate covariate;
    RecalibrationArgumentCollection RAC;

    @BeforeClass
    public void init() {
        RAC = new RecalibrationArgumentCollection();
        covariate = new CycleCovariate();
        covariate.initialize(RAC);
    }
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     *
     * @param table the GATKReportTable containing the arguments and its corresponding values
     * @return a RAC object properly initialized with all the objects in the table
     */
    private RecalibrationArgumentCollection initializeArgumentCollectionTable(GATKReportTable table) {
        final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();

        for ( int i = 0; i < table.getNumRows(); i++ ) {
            final String argument = table.get(i, "Argument").toString();
            Object value = table.get(i, RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
            if (value.equals("null"))
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Related Classes of org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection

  • org.broadinstitute.gatk.engine.report.GATKReportTable
  • org.broadinstitute.gatk.utils.recalibration.ContextCovariateUnitTest
  • org.broadinstitute.gatk.utils.recalibration.CycleCovariateUnitTest
  • org.broadinstitute.gatk.utils.recalibration.ReadCovariatesUnitTest
  • org.broadinstitute.gatk.utils.recalibration.ReadGroupCovariateUnitTest
  • org.broadinstitute.gatk.utils.recalibration.RecalibrationReport
  • org.broadinstitute.gatk.utils.recalibration.RecalibrationReportUnitTest
  • org.broadinstitute.gatk.utils.recalibration.RecalibrationTestUtils
  • org.broadinstitute.gatk.utils.recalibration.RepeatCovariatesUnitTest
  • org.broadinstitute.gatk.utils.exceptions.GATKException
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