Examples with BasicInputParser org.broadinstitute.hellbender.utils.text.parsers.BasicInputParser used on opensource projects

Example 1 with BasicInputParser

use of org.broadinstitute.hellbender.utils.text.parsers.BasicInputParser in project gatk by broadinstitute.

the class VectorPairHMMUnitTest method testLikelihoodsFromHaplotypes.

@Test(dataProvider = "JustHMMProvider")
public void testLikelihoodsFromHaplotypes(final PairHMM hmm, Boolean loaded) {
    // skip if not loaded
    if (!loaded.booleanValue()) {
        throw new SkipException("AVX PairHMM is not supported on this system or the library is not available");
    }
    BasicInputParser parser = null;
    try {
        parser = new BasicInputParser(true, new FileInputStream(pairHMMTestData));
    } catch (FileNotFoundException e) {
        Assert.fail("PairHMM test data not found : " + pairHMMTestData);
    }
    while (parser.hasNext()) {
        String[] tokens = parser.next();
        final Haplotype hap = new Haplotype(tokens[0].getBytes(), true);
        final byte[] bases = tokens[1].getBytes();
        final byte[] baseQuals = normalize(tokens[2].getBytes(), 6);
        final byte[] insertionQuals = normalize(tokens[3].getBytes());
        final byte[] deletionQuals = normalize(tokens[4].getBytes());
        final byte[] gcp = normalize(tokens[5].getBytes());
        final double expectedResult = Double.parseDouble(tokens[6]);
        final int readLength = bases.length;
        final GATKRead read = ArtificialReadUtils.createArtificialRead(bases, baseQuals, readLength + "M");
        ReadUtils.setInsertionBaseQualities(read, insertionQuals);
        ReadUtils.setDeletionBaseQualities(read, deletionQuals);
        final Map<GATKRead, byte[]> gpcs = new LinkedHashMap<>(readLength);
        gpcs.put(read, gcp);
        hmm.initialize(Arrays.asList(hap), null, 0, 0);
        hmm.computeLog10Likelihoods(matrix(Arrays.asList(hap)), Arrays.asList(read), gpcs);
        final double[] la = hmm.getLogLikelihoodArray();
        Assert.assertEquals(la[0], expectedResult, 1e-5, "Likelihood not in expected range.");
    }
    hmm.close();
}