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

Example 1 with FeatureInput

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

the class VariantAnnotatorEngineUnitTest method testCoverageAnnotationOnDbSnpSite.

@Test
public void testCoverageAnnotationOnDbSnpSite() throws Exception {
    final List<String> annotationGroupsToUse = Collections.emptyList();
    //good one
    final List<String> annotationsToUse = Arrays.asList(Coverage.class.getSimpleName());
    final List<String> annotationsToExclude = Collections.emptyList();
    final String path = publicTestDir + "Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf";
    final FeatureInput<VariantContext> dbSNPBinding = new FeatureInput<>(path, "dbsnp", Collections.emptyMap());
    final List<FeatureInput<VariantContext>> features = Collections.emptyList();
    final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude, dbSNPBinding, features);
    final Set<VCFHeaderLine> vcfAnnotationDescriptions = vae.getVCFAnnotationDescriptions();
    Assert.assertTrue(vcfAnnotationDescriptions.contains(VCFStandardHeaderLines.getInfoLine(VCFConstants.DBSNP_KEY)));
    final int alt = 5;
    final int ref = 3;
    final SimpleInterval loc = new SimpleInterval("1", 69428, 69428);
    final VariantContext vcRS = new FeatureDataSource<VariantContext>(path, null, 0, VariantContext.class).query(loc).next();
    final Allele refAllele = vcRS.getReference();
    final Allele altAllele = vcRS.getAlternateAllele(0);
    final VariantContext vcToAnnotate = makeVC(refAllele, altAllele, loc);
    final ReadLikelihoods<Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, altAllele, loc.getContig(), loc.getStart() - 5);
    final FeatureContext featureContext = when(mock(FeatureContext.class).getValues(dbSNPBinding, loc.getStart())).thenReturn(Arrays.<VariantContext>asList(vcRS)).getMock();
    final VariantContext resultVC = vae.annotateContext(vcToAnnotate, featureContext, null, likelihoods, a -> true);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.DEPTH_KEY), String.valueOf(ref + alt));
    Assert.assertEquals(resultVC.getID(), vcRS.getID());
}

Example 2 with FeatureInput

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

the class VariantAnnotatorEngineUnitTest method testCoverageAnnotationOnOverlapSite.

@Test
public void testCoverageAnnotationOnOverlapSite() throws Exception {
    final List<String> annotationGroupsToUse = Collections.emptyList();
    //good one
    final List<String> annotationsToUse = Arrays.asList(Coverage.class.getSimpleName());
    final List<String> annotationsToExclude = Collections.emptyList();
    final String path = publicTestDir + "Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf";
    final FeatureInput<VariantContext> dbSNPBinding = null;
    final String featureSourceName = "fred";
    //we'll just reuse the DBSnp file under a different name
    final FeatureInput<VariantContext> fredInput = new FeatureInput<>(path, featureSourceName, Collections.emptyMap());
    final List<FeatureInput<VariantContext>> features = Arrays.asList(fredInput);
    final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude, dbSNPBinding, features);
    final Set<VCFHeaderLine> vcfAnnotationDescriptions = vae.getVCFAnnotationDescriptions();
    Assert.assertFalse(vcfAnnotationDescriptions.contains(VCFStandardHeaderLines.getInfoLine(VCFConstants.DBSNP_KEY)));
    final VCFInfoHeaderLine fredHeaderLine = new VCFInfoHeaderLine(featureSourceName, 0, VCFHeaderLineType.Flag, featureSourceName + " Membership");
    Assert.assertTrue(vcfAnnotationDescriptions.contains(fredHeaderLine));
    final int alt = 5;
    final int ref = 3;
    final SimpleInterval loc = new SimpleInterval("1", 69428, 69428);
    final VariantContext vcRS = new FeatureDataSource<VariantContext>(path, null, 0, VariantContext.class).query(loc).next();
    final Allele refAllele = vcRS.getReference();
    final Allele altAllele = vcRS.getAlternateAllele(0);
    final VariantContext vcToAnnotate = makeVC(refAllele, altAllele, loc);
    final ReadLikelihoods<Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, altAllele, loc.getContig(), loc.getStart() - 5);
    final FeatureContext featureContext = when(mock(FeatureContext.class).getValues(fredInput, loc.getStart())).thenReturn(Arrays.<VariantContext>asList(vcRS)).getMock();
    final VariantContext resultVC = vae.annotateContext(vcToAnnotate, featureContext, null, likelihoods, a -> true);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.DEPTH_KEY), String.valueOf(ref + alt));
    Assert.assertEquals(resultVC.getID(), VCFConstants.EMPTY_ID_FIELD);
    Assert.assertTrue((boolean) resultVC.getCommonInfo().getAttribute(featureSourceName));
    Assert.assertNull(resultVC.getCommonInfo().getAttribute("does not exist"));
}

Example 3 with FeatureInput

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

the class VariantAnnotatorEngineUnitTest method testDBSNPONlyViaSpecialArg.

@Test(expectedExceptions = GATKException.class)
public void testDBSNPONlyViaSpecialArg() throws Exception {
    final List<String> annotationGroupsToUse = Collections.emptyList();
    //good one
    final List<String> annotationsToUse = Arrays.asList(Coverage.class.getSimpleName());
    final List<String> annotationsToExclude = Collections.emptyList();
    final File dbSNPFile = new File(publicTestDir + "Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf");
    final FeatureInput<VariantContext> dbSNPBinding = new FeatureInput<>(dbSNPFile.getAbsolutePath(), VCFConstants.DBSNP_KEY, Collections.emptyMap());
    final File fredFile = getTestFile("one_entry_source.vcf");
    final FeatureInput<VariantContext> fredInput = new FeatureInput<>(fredFile.getAbsolutePath(), VCFConstants.DBSNP_KEY, Collections.emptyMap());
    final List<FeatureInput<VariantContext>> features = Arrays.asList(fredInput);
    VariantAnnotatorEngine.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude, dbSNPBinding, features);
}

Example 4 with FeatureInput

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

the class VariantAnnotatorEngineUnitTest method testAllAnnotations.

@Test
public void testAllAnnotations() throws Exception {
    /**
         * exclude {@link StrandArtifact} until https://github.com/broadinstitute/gatk/issues/2797 is fixed
         * exclude {@link ReferenceBases} until https://github.com/broadinstitute/gatk/issues/2799 is fixed
         * */
    final List<String> annotationsToExclude = Arrays.asList("StrandArtifact", "ReferenceBases");
    final FeatureInput<VariantContext> dbSNPBinding = null;
    final List<FeatureInput<VariantContext>> features = Collections.emptyList();
    final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features);
    Assert.assertFalse(vae.getVCFAnnotationDescriptions().contains(null));
    final int alt = 5;
    final int ref = 3;
    final Allele refAllele = Allele.create("A", true);
    final Allele altAllele = Allele.create("T");
    final ReadLikelihoods<Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, altAllele);
    final VariantContext resultVC = vae.annotateContext(makeVC(refAllele, altAllele), new FeatureContext(), null, likelihoods, a -> true);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.DEPTH_KEY), String.valueOf(ref + alt));
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.ALLELE_COUNT_KEY), 1);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY), 1.0 / 2);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.ALLELE_NUMBER_KEY), 2);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.FISHER_STRAND_KEY), FisherStrand.makeValueObjectForAnnotation(new int[][] { { ref, 0 }, { alt, 0 } }));
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.NOCALL_CHROM_KEY), 0);
    Assert.assertNull(resultVC.getCommonInfo().getAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY));
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY), RMSMappingQuality.formattedValue(0.0));
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.MAPPING_QUALITY_ZERO_KEY), MappingQualityZero.formattedValue(8));
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.SAMPLE_LIST_KEY), "sample1");
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.STRAND_ODDS_RATIO_KEY), StrandOddsRatio.formattedValue(StrandOddsRatio.calculateSOR(new int[][] { { ref, 0 }, { alt, 0 } })));
}

Example 5 with FeatureInput

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

the class VariantAnnotatorEngineUnitTest method testCoverageAnnotationViaEngine.

@Test
public void testCoverageAnnotationViaEngine() throws Exception {
    final File file = new File(publicTestDir + "Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf");
    final FeatureInput<VariantContext> dbSNPBinding = new FeatureInput<>(file.getAbsolutePath(), "dbsnp", Collections.emptyMap());
    final List<String> annotationGroupsToUse = Collections.emptyList();
    final List<String> annotationsToUse = Arrays.asList(Coverage.class.getSimpleName(), DepthPerAlleleBySample.class.getSimpleName(), SampleList.class.getSimpleName());
    final List<String> annotationsToExclude = Collections.emptyList();
    final List<FeatureInput<VariantContext>> features = Collections.emptyList();
    final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude, dbSNPBinding, features);
    final int alt = 5;
    final int ref = 3;
    final Allele refAllele = Allele.create("A", true);
    final Allele altAllele = Allele.create("T");
    final ReadLikelihoods<Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, altAllele);
    final VariantContext resultVC = vae.annotateContext(makeVC(refAllele, altAllele), new FeatureContext(), null, likelihoods, ann -> ann instanceof Coverage || ann instanceof DepthPerAlleleBySample);
    Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.DEPTH_KEY), String.valueOf(ref + alt));
    Assert.assertEquals(resultVC.getGenotype(0).getAD(), new int[] { ref, alt });
    //skipped because we only asked for Coverage and DepthPerAlleleBySample
    Assert.assertFalse(resultVC.getCommonInfo().hasAttribute(GATKVCFConstants.SAMPLE_LIST_KEY));
}