Java Code Examples for htsjdk.variant.variantcontext.Genotype#getAnyAttribute()

The following examples show how to use htsjdk.variant.variantcontext.Genotype#getAnyAttribute() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: StrandBiasTest.java    From gatk with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
@SuppressWarnings("unchecked")
public static int[] getStrandCounts(final Genotype g) {
    int[] data;
    if ( g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY).getClass().equals(String.class)) {
        final String sbbsString = (String)g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY);
        data = encodeSBBS(sbbsString);
    } else if (g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY).getClass().equals(ArrayList.class)) {
       if (((ArrayList<Object>)g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY)).get(0) instanceof Integer) {
            data = encodeSBBS((ArrayList<Integer>) g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY));
        }
        else if (((ArrayList<Object>)g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY)).get(0) instanceof String) {
            final List<Integer> sbbsList = new ArrayList<>();
            for (final Object o : (ArrayList<Object>) g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY)) {
                sbbsList.add(Integer.parseInt(o.toString()));
            }
            data = encodeSBBS(sbbsList);
        } else {
            throw new GATKException("Unexpected " + GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY + " type");
        }

    } else {
        throw new GATKException("Unexpected " + GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY + " type");
    }
    return data;
}
Example 2
Source File: VcfToAdpc.java    From picard with MIT License 5 votes vote down vote up 
private Float getFloatAttribute(final Genotype genotype, final String key) {
    final Object value = genotype.getAnyAttribute(key);
    if (value != null) {
        return Float.parseFloat(value.toString());
    }
    return null;
}
Example 3
Source File: VcfToAdpc.java    From picard with MIT License 5 votes vote down vote up 
private Object getRequiredAttribute(Genotype genotype, final String key) {
    final Object value = genotype.getAnyAttribute(key);
    if (value == null) {
        throw new PicardException("Unable to find attribute " + key + " in VCF Genotype field.  Is this an Arrays VCF file?");
    }
    return value;
}
Example 4
Source File: GermlineFilters.java    From hmftools with GNU General Public License v3.0 4 votes vote down vote up 
public static double getDoubleValue(final Genotype data, final String field)
{
    Object value = data.getAnyAttribute(field);
    return value != null ? Double.parseDouble((String)value) : 0.0;
}
Example 5
Source File: GermlineFilters.java    From hmftools with GNU General Public License v3.0 4 votes vote down vote up 
public static int getIntValue(final Genotype data, final String field)
{
    Object value = data.getAnyAttribute(field);
    return value != null ? Integer.parseInt((String)value) : 0;
}
Example 6
Source File: EvaluateCopyNumberTriStateCallsIntegrationTest.java    From gatk-protected with BSD 3-Clause "New" or "Revised" License 4 votes vote down vote up 
private void checkOutputTruthConcordance(final File truthFile, final File targetsFile, final File vcfOutput, final EvaluationFiltersArgumentCollection filteringOptions) {
    final List<VariantContext> truthVariants = readVCFFile(truthFile);
    final List<VariantContext> outputVariants = readVCFFile(vcfOutput);
    final Set<String> outputSamples = outputVariants.get(0).getSampleNames();
    final TargetCollection<Target> targets = TargetArgumentCollection.readTargetCollection(targetsFile);

    for (final VariantContext truth : truthVariants) {
        final List<Target> overlappingTargets = targets.targets(truth);
        final List<VariantContext> overlappingOutput = outputVariants.stream()
                .filter(vc -> new SimpleInterval(vc).overlaps(truth))
                .collect(Collectors.toList());

        if (overlappingTargets.isEmpty()) {
            Assert.assertTrue(overlappingOutput.isEmpty());
            continue;
        }
        Assert.assertFalse(overlappingOutput.isEmpty());
        Assert.assertEquals(overlappingOutput.stream().filter(vc -> new SimpleInterval(truth).equals(new SimpleInterval(vc))).count(), 1);
        @SuppressWarnings("all")
        final Optional<VariantContext> prospectiveMatchingOutput = overlappingOutput.stream()
                .filter(vc -> new SimpleInterval(truth).equals(new SimpleInterval(vc)))
                .findFirst();
        Assert.assertTrue(prospectiveMatchingOutput.isPresent());
        final VariantContext matchingOutput = prospectiveMatchingOutput.get();
        final int[] truthAC = calculateACFromTruth(truth);
        final long truthAN = MathUtils.sum(truthAC);
        final double[] truthAF = IntStream.of(Arrays.copyOfRange(truthAC, 1, truthAC.length)).mapToDouble(d -> d / (double) truthAN).toArray();
        Assert.assertEquals(matchingOutput.getAttributeAsInt(VariantEvaluationContext.TRUTH_ALLELE_NUMBER_KEY, -1), truthAN);
        assertEquals(GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(matchingOutput, VariantEvaluationContext.TRUTH_ALLELE_FREQUENCY_KEY, () -> new double[2], 0.0),
                truthAF, 0.001);
        assertOutputVariantFilters(filteringOptions, overlappingTargets, matchingOutput, truthAF);
        for (final String sample : outputSamples) {
            final Genotype outputGenotype = matchingOutput.getGenotype(sample);
            final Genotype truthGenotype = truth.getGenotype(sample);
            final int truthCN = GATKProtectedVariantContextUtils.getAttributeAsInt(truthGenotype, ConvertGSVariantsToSegments.GS_COPY_NUMBER_FORMAT, -1);
            final int truthGT = GATKProtectedVariantContextUtils.getAttributeAsInt(outputGenotype, VariantEvaluationContext.TRUTH_GENOTYPE_KEY, -1);
            final Object truthQualObject = outputGenotype.getAnyAttribute(VariantEvaluationContext.TRUTH_QUALITY_KEY);
            Assert.assertNotNull(truthQualObject, "" + truthGenotype);
            final double truthQual = Double.parseDouble(String.valueOf(truthQualObject));
            if (truthQual < filteringOptions.minimumTruthSegmentQuality) {
                Assert.assertEquals(outputGenotype.getFilters(),EvaluationFilter.LowQuality.acronym);
            } else {
                Assert.assertTrue(outputGenotype.getFilters() == null || outputGenotype.getFilters().equals(VCFConstants.PASSES_FILTERS_v4));
            }
            final double[] truthPosteriors = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(truthGenotype, ConvertGSVariantsToSegments.GS_COPY_NUMBER_POSTERIOR,
                    () -> new double[0], Double.NEGATIVE_INFINITY);
            final double truthDelPosterior = MathUtils.log10SumLog10(truthPosteriors, 0, EvaluateCopyNumberTriStateCalls.REFERENCE_COPY_NUMBER_DEFAULT);
            final double truthRefPosterior = truthPosteriors[EvaluateCopyNumberTriStateCalls.REFERENCE_COPY_NUMBER_DEFAULT];
            final double truthDupPosterior = truthPosteriors.length < EvaluateCopyNumberTriStateCalls.REFERENCE_COPY_NUMBER_DEFAULT ? Double.NEGATIVE_INFINITY : MathUtils.log10SumLog10(truthPosteriors, EvaluateCopyNumberTriStateCalls.REFERENCE_COPY_NUMBER_DEFAULT + 1, truthPosteriors.length);

            final CopyNumberTriStateAllele truthAllele = truthGT == -1 ? null : CopyNumberTriStateAllele.ALL_ALLELES.get(truthGT);
            if (truthCN < EvaluateCopyNumberTriStateCalls.REFERENCE_COPY_NUMBER_DEFAULT) {
                Assert.assertEquals(truthAllele, CopyNumberTriStateAllele.DEL);
                Assert.assertEquals(truthQual * -.1, MathUtils.log10SumLog10(new double[] {truthRefPosterior, truthDupPosterior}), 0.01);
            } else if (truthCN > EvaluateCopyNumberTriStateCalls.REFERENCE_COPY_NUMBER_DEFAULT) {
                Assert.assertEquals(truthAllele, CopyNumberTriStateAllele.DUP);
                Assert.assertEquals(truthQual * -.1, MathUtils.log10SumLog10(new double[] {truthDelPosterior, truthRefPosterior}), 0.01, "" + truthGenotype + " " + outputGenotype);
            } else {
                Assert.assertEquals(truthAllele, CopyNumberTriStateAllele.REF);
                Assert.assertEquals(truthQual * -.1, MathUtils.log10SumLog10(new double[] {truthDelPosterior, truthDupPosterior}), 0.01);
            }
            final double outputTruthFraction = GATKProtectedVariantContextUtils.getAttributeAsDouble(outputGenotype, VariantEvaluationContext.TRUTH_COPY_FRACTION_KEY, -1);
            final double inputTruthFraction = GATKProtectedVariantContextUtils.getAttributeAsDouble(truthGenotype, ConvertGSVariantsToSegments.GS_COPY_NUMBER_FRACTION, -1);
            Assert.assertEquals(outputTruthFraction, inputTruthFraction, 0.01);
        }
    }
}