Examples with CovariateKeyCache org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache used on opensource projects

Example 1 with CovariateKeyCache

use of org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache in project gatk by broadinstitute.

the class ReadRecalibrationInfoUnitTest method testReadInfo.

@Test(dataProvider = "InfoProvider")
public void testReadInfo(final int readLength, final boolean includeIndelErrors) {
    final ReadCovariates covariates = new ReadCovariates(readLength, 2, new CovariateKeyCache());
    final byte[] bases = new byte[readLength];
    final byte[] baseQuals = new byte[readLength];
    final byte[] insertionQuals = new byte[readLength];
    final byte[] deletionQuals = new byte[readLength];
    final boolean[] skips = new boolean[readLength];
    final double[] snpErrors = new double[readLength];
    final double[] insertionErrors = new double[readLength];
    final double[] deletionsErrors = new double[readLength];
    for (int i = 0; i < readLength; i++) {
        bases[i] = 'A';
        baseQuals[i] = (byte) (i % SAMUtils.MAX_PHRED_SCORE);
        insertionQuals[i] = (byte) ((i + 1) % SAMUtils.MAX_PHRED_SCORE);
        deletionQuals[i] = (byte) ((i + 2) % SAMUtils.MAX_PHRED_SCORE);
        skips[i] = i % 2 == 0;
        snpErrors[i] = 1.0 / (i + 1);
        insertionErrors[i] = 0.5 / (i + 1);
        deletionsErrors[i] = 0.3 / (i + 1);
    }
    final EnumMap<EventType, double[]> errors = new EnumMap<>(EventType.class);
    errors.put(EventType.BASE_SUBSTITUTION, snpErrors);
    errors.put(EventType.BASE_INSERTION, insertionErrors);
    errors.put(EventType.BASE_DELETION, deletionsErrors);
    final EnumMap<EventType, byte[]> quals = new EnumMap<>(EventType.class);
    quals.put(EventType.BASE_SUBSTITUTION, baseQuals);
    quals.put(EventType.BASE_INSERTION, insertionQuals);
    quals.put(EventType.BASE_DELETION, deletionQuals);
    final GATKRead read = ArtificialReadUtils.createArtificialRead(bases, baseQuals, readLength + "M");
    if (includeIndelErrors) {
        ReadUtils.setInsertionBaseQualities(read, insertionQuals);
        ReadUtils.setDeletionBaseQualities(read, deletionQuals);
    }
    final ReadRecalibrationInfo info = new ReadRecalibrationInfo(read, covariates, skips, snpErrors, insertionErrors, deletionsErrors);
    Assert.assertEquals(info.getCovariatesValues(), covariates);
    Assert.assertEquals(info.getRead(), read);
    for (int i = 0; i < readLength; i++) {
        Assert.assertEquals(info.skip(i), skips[i]);
        for (final EventType et : EventType.values()) {
            Assert.assertEquals(info.getErrorFraction(et, i), errors.get(et)[i]);
            final byte expectedQual = et == EventType.BASE_SUBSTITUTION || includeIndelErrors ? quals.get(et)[i] : ReadUtils.DEFAULT_INSERTION_DELETION_QUAL;
            Assert.assertEquals(info.getQual(et, i), expectedQual);
        }
    }
}