FingerprintCheckerTest.java

package picard.fingerprint;

import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import picard.vcf.VcfTestUtils;

import java.io.File;
import java.io.IOException;
import java.util.*;

/**
 * Created by farjoun on 8/27/15.
 */
public class FingerprintCheckerTest {

    private final double maf = 0.4;
    private final Snp snp = new Snp("test", "chr1", 1, (byte) 'A', (byte) 'C', maf, Collections.singletonList("dummy"));
    private final HaplotypeBlock hb = new HaplotypeBlock(maf);

    private static final double DELTA = 1e-6;

    private static final File TEST_DATA_DIR = new File("testdata/picard/fingerprint/");
    private static final File SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING = new File(TEST_DATA_DIR, "Homo_sapiens_assembly19.haplotype_database.subset.txt");

    @BeforeClass
    public void setup() {
        hb.addSnp(snp);
    }

    @Test
    public void testRandomSublist() throws Exception {

        final List<Integer> list = new ArrayList<>();
        list.add(1);
        list.add(2);
        list.add(3);

        Assert.assertEquals(list, FingerprintChecker.randomSublist(list, 3));
        Assert.assertEquals(list, FingerprintChecker.randomSublist(list, 4));
        Assert.assertEquals(FingerprintChecker.randomSublist(list, 2).size(), 2);
    }

    @DataProvider(name = "pLoH")
    public Iterator<Object[]> pLohData() {
        final List<Object[]> listOfDoubles = new ArrayList<>();

        for (int i = 1; i < 20; i++) {
            listOfDoubles.add(new Object[]{i / 40D});
        }
        return listOfDoubles.iterator();
    }

    @Test(dataProvider = "pLoH")
    public void testMatchResults(final double pLoH) {

        final Fingerprint fpObserved = new Fingerprint("test", null, "noop");
        final Fingerprint fpExpected = new Fingerprint("test", null, "noop");

        final HaplotypeProbabilities hpHet = new HaplotypeProbabilitiesFromGenotype(snp, hb, 0.0001, 1.0, 0.0001);
        final HaplotypeProbabilities hpHomRef = new HaplotypeProbabilitiesFromGenotype(snp, hb, 1.0, 0.00001, 0.000000001);

        // Expected is a het
        fpExpected.add(hpHet);

        // Observed is a hom, so possible scenario is that observed is tumor, and expected is normal
        fpObserved.add(hpHomRef);

        // get match results using pLOD
        final MatchResults mr = FingerprintChecker.calculateMatchResults(fpObserved, fpExpected, 0.01, pLoH);

        // make sure that it's more likely to be the same sample, if the observed is "tumor" and the expected is "normal"
        Assert.assertTrue(mr.getLodTN() > mr.getLOD());

        // make sure that the regular LOD is negative (we're comparing a HET to a HOM)
        Assert.assertTrue(mr.getLOD() < 0);

        // make sure that it's more likely to be tumor/normal rather than normal/tumor
        // (a hom normal isn't expected to be measured as a het in the tumor)
        Assert.assertTrue(mr.getLodTN() > mr.getLodNT());
    }

    @DataProvider(name = "checkFingerprintsVcfDataProvider")
    public Object[][] testCheckFingerprintsVcfDataProvider() {
        return new Object[][] {
                {new File(TEST_DATA_DIR, "NA12891.vcf"), new File(TEST_DATA_DIR, "NA12891.fp.vcf"), "NA12891", "NA12891", -0.02128, -1.026742, 1.005462},
                {new File(TEST_DATA_DIR, "NA12892.vcf"), new File(TEST_DATA_DIR, "NA12892.fp.vcf"), "NA12892", "NA12892", -0.021945, -1.08308, 1.061135},
                {new File(TEST_DATA_DIR, "NA12891.vcf"), new File(TEST_DATA_DIR, "NA12892.fp.vcf"), "NA12891", "NA12892", -5.941691, -1.026742, -4.914948},
                {new File(TEST_DATA_DIR, "NA12892.vcf"), new File(TEST_DATA_DIR, "NA12891.fp.vcf"), "NA12892", "NA12891", -5.998029, -1.08308, -4.914948}
        };
    }

    @Test(dataProvider = "checkFingerprintsVcfDataProvider")
    public void testCheckFingerprints(File vcfFile,  File genotypesFile,  String observedSampleAlias,  String expectedSampleAlias,
                                      double llExpectedSample, double llRandomSample, double lodExpectedSample) throws IOException {
        final File indexedInputVcf = VcfTestUtils.createTemporaryIndexedVcfFromInput(vcfFile, "fingerprintcheckertest.tmp.");
        final File indexedGenotypesVcf = VcfTestUtils.createTemporaryIndexedVcfFromInput(genotypesFile, "fingerprintcheckertest.tmp.");

        final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);
        final List<FingerprintResults> results = fpChecker.checkFingerprints(Collections.singletonList(indexedInputVcf),
                Collections.singletonList(indexedGenotypesVcf),
                observedSampleAlias,
                expectedSampleAlias);
        Assert.assertEquals(results.size(), 1);
        final FingerprintResults fpr = results.get(0);
        Assert.assertNull(fpr.getReadGroup());
        Assert.assertEquals(fpr.getSampleAlias(), observedSampleAlias);
        final MatchResults mr = fpr.getMatchResults().first();
        Assert.assertEquals(mr.getSample(), expectedSampleAlias);
        Assert.assertEquals(mr.getSampleLikelihood(), llExpectedSample, DELTA);
        Assert.assertEquals(mr.getPopulationLikelihood(), llRandomSample, DELTA);
        Assert.assertEquals(mr.getLOD(), lodExpectedSample, DELTA);
    }
}