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

@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;
}
 

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;
}
 

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;
}
 

public static double getDoubleValue(final Genotype data, final String field)
{
    Object value = data.getAnyAttribute(field);
    return value != null ? Double.parseDouble((String)value) : 0.0;
}
 

public static int getIntValue(final Genotype data, final String field)
{
    Object value = data.getAnyAttribute(field);
    return value != null ? Integer.parseInt((String)value) : 0;
}
 

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);
        }
    }
}