Examples of org.broadinstitute.gatk.engine.ReadProperties

org.broadinstitute.gatk.engine.ReadProperties
A data structure containing information about the reads data sources as well as information about how they should be downsampled, sorted, and filtered.

    public void initialize(final GenomeAnalysisEngine engine) {
        header = engine.getSAMFileHeader();
        ValidationExclusion validationExclusions = null;
        final SAMDataSource rds = engine.getReadsDataSource();
        if (rds != null) {
          final ReadProperties rps = rds.getReadsInfo();
          if (rps != null) {
            validationExclusions = rps.getValidationExclusionList();
          }
        }
        if (validationExclusions == null) {
            allowNCigars = false;
        } else {

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        }


        mergedHeader = readers.getMergedHeader();
        hasReadGroupCollisions = readers.hasReadGroupCollisions();


        readProperties = new ReadProperties(
                samFiles,
                mergedHeader,
                sortOrder,
                useOriginalBaseQualities,
                strictness,

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    public void testXandEQOperators() {
        final byte[] bases1 = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
        final byte[] bases2 = new byte[] {'A','A','A','C','A','A','A','A','A','C'};


        // create a test version of the Reads object
        ReadProperties readAttributes = createTestReadProperties();


        GATKSAMRecord r1 = ArtificialSAMUtils.createArtificialRead(header,"r1",0,1,10);
        r1.setReadBases(bases1);
        r1.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20});
        r1.setCigarString("10M");

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    public void testIndelsInRegularPileup() {
        final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
        final byte[] indelBases = new byte[] {'A','A','A','A','C','T','A','A','A','A','A','A'};


        // create a test version of the Reads object
        ReadProperties readAttributes = createTestReadProperties();


        GATKSAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
        before.setReadBases(bases);
        before.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20});
        before.setCigarString("10M");

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    @Test(enabled = false && ! DEBUG)
    public void testWholeIndelReadInIsolation() {
        final int firstLocus = 44367789;


        // create a test version of the Reads object
        ReadProperties readAttributes = createTestReadProperties();


        GATKSAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76);
        indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76));
        indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
        indelOnlyRead.setCigarString("76I");

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    public static ReadProperties createTestReadProperties() {
        return createTestReadProperties(null, false);
    }


    public static ReadProperties createTestReadProperties( DownsamplingMethod downsamplingMethod, final boolean keepReads ) {
        return new ReadProperties(
                Collections.<SAMReaderID>emptyList(),
                new SAMFileHeader(),
                SAMFileHeader.SortOrder.coordinate,
                false,
                ValidationStringency.STRICT,

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Related Classes of org.broadinstitute.gatk.engine.ReadProperties

org.broadinstitute.gatk.engine.arguments.ValidationExclusion

org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource

org.broadinstitute.gatk.engine.filters.MalformedReadFilter

org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByStateBaseTest

org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByStateUnitTest

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