Examples with ReferenceContext org.broadinstitute.hellbender.engine.ReferenceContext used on opensource projects

Example 16 with ReferenceContext

use of org.broadinstitute.hellbender.engine.ReferenceContext in project gatk by broadinstitute.

the class ChromosomeCountsUnitTest method testVC.

@Test
public void testVC() throws Exception {
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final InfoFieldAnnotation ann = new ChromosomeCounts();
    final Map<String, Object> annotate = ann.annotate(referenceContext, vc, null);
    //two hets
    Assert.assertEquals(annotate.get(VCFConstants.ALLELE_NUMBER_KEY), 4);
    Assert.assertEquals(annotate.get(VCFConstants.ALLELE_COUNT_KEY), 2);
    Assert.assertEquals(annotate.get(VCFConstants.ALLELE_FREQUENCY_KEY), 0.5);
    Assert.assertEquals(ann.getDescriptions(), Arrays.asList(ChromosomeCounts.descriptions));
    Assert.assertEquals(ann.getKeyNames(), Arrays.asList(ChromosomeCounts.keyNames));
}

Example 17 with ReferenceContext

use of org.broadinstitute.hellbender.engine.ReferenceContext in project gatk by broadinstitute.

the class ClippingRankSumTestUnitTest method testClipping.

@Test
public void testClipping() {
    final int[] refHardClips = { 10, 0 };
    final int[] altHardClips = { 1, 2 };
    final List<GATKRead> refReads = Arrays.stream(refHardClips).mapToObj(i -> makeRead(i)).collect(Collectors.toList());
    final List<GATKRead> altReads = Arrays.stream(altHardClips).mapToObj(i -> makeRead(i)).collect(Collectors.toList());
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods(SAMPLE_1, refReads, altReads, -100.0, -100.0, REF, ALT);
    final ReferenceContext ref = null;
    final VariantContext vc = makeVC(REF, ALT);
    final InfoFieldAnnotation ann = new ClippingRankSumTest();
    final MannWhitneyU mannWhitneyU = new MannWhitneyU();
    final Map<String, Object> annotate = ann.annotate(ref, vc, likelihoods);
    final double zScore = mannWhitneyU.test(new double[] { altHardClips[0], altHardClips[1] }, new double[] { refHardClips[0], refHardClips[1] }, MannWhitneyU.TestType.FIRST_DOMINATES).getZ();
    final String zScoreStr = String.format("%.3f", zScore);
    Assert.assertEquals(annotate.get(GATKVCFConstants.CLIPPING_RANK_SUM_KEY), zScoreStr);
    Assert.assertEquals(ann.getDescriptions().size(), 1);
    Assert.assertEquals(ann.getDescriptions().get(0).getID(), GATKVCFConstants.CLIPPING_RANK_SUM_KEY);
    Assert.assertEquals(ann.getKeyNames().size(), 1);
    Assert.assertEquals(ann.getKeyNames().get(0), GATKVCFConstants.CLIPPING_RANK_SUM_KEY);
}

Example 18 with ReferenceContext

use of org.broadinstitute.hellbender.engine.ReferenceContext in project gatk by broadinstitute.

the class CoverageUnitTest method testLikelihoodsEmpty.

@Test
public void testLikelihoodsEmpty() throws Exception {
    final List<GATKRead> reads = new ArrayList<>();
    final Map<String, List<GATKRead>> readsBySample = ImmutableMap.of("sample1", reads);
    final org.broadinstitute.hellbender.utils.genotyper.SampleList sampleList = new IndexedSampleList(Arrays.asList("sample1"));
    final AlleleList<Allele> alleleList = new IndexedAlleleList<>(Arrays.asList(Allele.NO_CALL));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new Coverage().annotate(referenceContext, vc, likelihoods);
    Assert.assertTrue(annotate.isEmpty());
}

Example 19 with ReferenceContext

use of org.broadinstitute.hellbender.engine.ReferenceContext in project gatk by broadinstitute.

the class BaseQualityRankSumTestUnitTest method testBaseQualRawAnnotate.

@Test
public void testBaseQualRawAnnotate() {
    final AS_RankSumTest ann = new AS_BaseQualityRankSumTest();
    final String key1 = GATKVCFConstants.AS_RAW_BASE_QUAL_RANK_SUM_KEY;
    final String key2 = GATKVCFConstants.AS_BASE_QUAL_RANK_SUM_KEY;
    final int[] altBaseQuals = { 10, 20 };
    final int[] refBaseQuals = { 50, 60 };
    final List<GATKRead> refReads = Arrays.stream(refBaseQuals).mapToObj(i -> makeRead(i)).collect(Collectors.toList());
    final List<GATKRead> altReads = Arrays.stream(altBaseQuals).mapToObj(i -> makeRead(i)).collect(Collectors.toList());
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods(SAMPLE_1, refReads, altReads, -100.0, -100.0, REF, ALT);
    final ReferenceContext ref = null;
    final VariantContext vc = makeVC(REF, ALT);
    final Map<String, Object> annotateRaw = ann.annotateRawData(ref, vc, likelihoods);
    final Map<String, Object> annotateNonRaw = ann.annotate(ref, vc, likelihoods);
    final String expectedAnnotation = refBaseQuals[0] + ",1," + refBaseQuals[1] + ",1" + AS_RankSumTest.PRINT_DELIM + altBaseQuals[0] + ",1," + altBaseQuals[1] + ",1";
    Assert.assertEquals(annotateRaw.get(key1), expectedAnnotation);
    Assert.assertEquals(annotateNonRaw.get(key1), expectedAnnotation);
    Assert.assertEquals(ann.getDescriptions().size(), 1);
    Assert.assertEquals(ann.getDescriptions().get(0).getID(), key1);
    Assert.assertEquals(ann.getKeyNames().size(), 1);
    Assert.assertEquals(ann.getKeyNames().get(0), key2);
}

Example 20 with ReferenceContext

use of org.broadinstitute.hellbender.engine.ReferenceContext in project gatk by broadinstitute.

the class DepthPerSampleHCUnitTest method testNoReads.

@Test
public void testNoReads() {
    final Allele Aref = Allele.create("A", true);
    final Allele C = Allele.create("C");
    final List<Allele> AC = Arrays.asList(Aref, C);
    final ReferenceContext rc = new ReferenceContext();
    final GenotypeBuilder gb = new GenotypeBuilder("sample", AC).DP(10).AD(new int[] { 5, 5 });
    final Genotype g = gb.make();
    final List<GATKRead> reads = new ArrayList<>();
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods("sample", reads, -100.0, Aref, C);
    final VariantContext vc = new VariantContextBuilder("test", "20", 10, 10, AC).genotypes(Arrays.asList(g)).make();
    new DepthPerSampleHC().annotate(rc, vc, g, gb, likelihoods);
    Assert.assertEquals(gb.make().getDP(), 0);
}