Package org.broadinstitute.gatk.utils.sam

Examples of org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord

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        final String[] readGroups = {"RG1", "RG2", "RGbla"};
        for (int idx = 0; idx < NUM_READS; idx++) {
            for (final String rgs : readGroups) {
                final int length = 10 + rnd.nextInt(100); // random read length, at least 10 bp long
                final GATKSAMRecord read = ReadUtils.createRandomRead(length, false);
                final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(rgs);
                rg.setPlatform("illumina");
                read.setReadGroup(rg);
                read.setReadNegativeStrandFlag(rnd.nextBoolean());
                final byte[] mQuals = read.getBaseQualities(EventType.BASE_SUBSTITUTION);
                final byte[] iQuals = read.getBaseQualities(EventType.BASE_INSERTION);
                final byte[] dQuals = read.getBaseQualities(EventType.BASE_DELETION);
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        for (final Covariate cov : requiredCovariates)
            requestedCovariates[covariateIndex++] = cov;
        for (final Covariate cov : optionalCovariates)
            requestedCovariates[covariateIndex++] = cov;

        final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("id");
        rg.setPlatform("illumina");
        final GATKSAMRecord read = ReadUtils.createRandomRead(length, false);
        read.setReadGroup(rg);
        final byte [] readQuals = new byte[length];
        for (int i = 0; i < length; i++)
            readQuals[i] = 20;
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    }

    @Test(enabled = true)
    public void testSingleRecord() {
        final String expected = "SAMPLE.1";
        GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("MY.ID");
        rg.setPlatformUnit(expected);
        runTest(rg, expected, covariate);
    }
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    }

    @Test(enabled = true)
    public void testMissingPlatformUnit() {
        final String expected = "MY.7";
        GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(expected);
        runTest(rg, expected, covariate);
    }
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        final RecalibrationArgumentCollection forcedRAC = new RecalibrationArgumentCollection();
        forcedRAC.FORCE_READGROUP = "FOO";
        final ReadGroupCovariate forcedCovariate = new ReadGroupCovariate();
        forcedCovariate.initialize(forcedRAC);

        final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("NOT_FOO");
        runTest(rg, "FOO", forcedCovariate);
    }
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    @Test(enabled = true)
    public void testSimpleCycles() {
        short readLength = 10;
        GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
        read.setReadPairedFlag(true);
        read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
        read.getReadGroup().setPlatform("illumina");

        ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
        covariate.recordValues(read, readCovariates);
        verifyCovariateArray(readCovariates.getMismatchesKeySet(), 1, (short) 1);
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    @Test(enabled = true, expectedExceptions={UserException.class})
    public void testMoreThanMaxCycleFails() {
        int readLength = RAC.MAXIMUM_CYCLE_VALUE + 1;
        GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
        read.setReadPairedFlag(true);
        read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
        read.getReadGroup().setPlatform("illumina");

        ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
        covariate.recordValues(read, readCovariates);
    }
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    @Test(enabled = true)
    public void testMaxCyclePasses() {
        int readLength = RAC.MAXIMUM_CYCLE_VALUE;
        GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
        read.setReadPairedFlag(true);
        read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
        read.getReadGroup().setPlatform("illumina");

        ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
        covariate.recordValues(read, readCovariates);
    }
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    ReferenceConfidenceModel model;

    @BeforeClass
    public void setUp() throws Exception {
        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
        rg = new GATKSAMReadGroupRecord(RGID);
        rg.setSample(sample);
        header.addReadGroup(rg);
        parser = new GenomeLocParser(header.getSequenceDictionary());
    }
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     *
     * @param read The read to adjust
     * @param RAC  The list of shared command line arguments
     */
    public static void parsePlatformForRead(final GATKSAMRecord read, final RecalibrationArgumentCollection RAC) {
        GATKSAMReadGroupRecord readGroup = read.getReadGroup();

        if (RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
            readGroup.setPlatform(RAC.FORCE_PLATFORM);
        }

        if (readGroup.getPlatform() == null) {
            if (RAC.DEFAULT_PLATFORM != null) {
                if (!warnUserNullPlatform) {
                    Utils.warnUser("The input .bam file contains reads with no platform information. " +
                            "Defaulting to platform = " + RAC.DEFAULT_PLATFORM + ". " +
                            "First observed at read with name = " + read.getReadName());
                    warnUserNullPlatform = true;
                }
                readGroup.setPlatform(RAC.DEFAULT_PLATFORM);
            }
            else {
                throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName());
            }
        }
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Related Classes of org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord

  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMReaders
  • org.broadinstitute.gatk.tools.walkers.genotyper.ArtificialReadPileupTestProvider
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceModelUnitTest
  • org.broadinstitute.gatk.utils.fragments.FragmentUtilsUnitTest
  • org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByStateUnitTest
  • org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByStateUnitTest$WeakReadTrackingIterator
  • org.broadinstitute.gatk.utils.recalibration.CycleCovariateUnitTest
  • org.broadinstitute.gatk.utils.recalibration.ReadCovariatesUnitTest
  • org.broadinstitute.gatk.utils.recalibration.ReadGroupCovariateUnitTest
  • org.broadinstitute.gatk.utils.recalibration.RecalibrationReportUnitTest
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