htsjdk.variant.variantcontext.Allele#equals

Source File: GencodeFuncotationFactory.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

/**
 * Determines the variant type based on the given reference allele and alternate allele.
 * @param refAllele The reference {@link Allele} for this variant.
 * @param altAllele The alternate {@link Allele} for this variant.
 * @return A {@link GencodeFuncotation.VariantType} representing the variation type between the given reference and alternate {@link Allele}.
 * Spanning deletions and no calls will get a type of {@link org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantType#NA}
 */
@VisibleForTesting
static GencodeFuncotation.VariantType getVariantType( final Allele refAllele, final Allele altAllele ) {

    if ( altAllele.length() > refAllele.length() ) {
        return GencodeFuncotation.VariantType.INS;
    }
    else if (altAllele.equals(Allele.SPAN_DEL) || altAllele.equals(Allele.NO_CALL) || altAllele.isSymbolic() ) {
        return GencodeFuncotation.VariantType.NA;
    }
    else if (altAllele.length() < refAllele.length()) {
        return GencodeFuncotation.VariantType.DEL;
    }
    else {
        // We know they are the same length, now we just need to check one of them:
        switch (refAllele.length()) {
            case 1:  return GencodeFuncotation.VariantType.SNP;
            case 2:  return GencodeFuncotation.VariantType.DNP;
            case 3:  return GencodeFuncotation.VariantType.TNP;
            default: return GencodeFuncotation.VariantType.ONP;
        }
    }
}

Source File: GencodeFuncotationFactory.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

/**
 * Checks the given variant alt allele for whether it's a special case.
 * If so, will create the appropriate funcotation for that case.
 * @param variant {@link VariantContext} for the given {@code altAllele}.
 * @param altAllele The alternate {@link Allele} to be checked for special cases.
 * @param reference {@link ReferenceContext} supporting the given {@code variant}.
 * @param transcript {@link GencodeGtfTranscriptFeature} containing the given {@code variant}.
 * @return A {@link GencodeFuncotation} for the given special case alt allele, or {@code null} if the allele is not a special case.
 */
private GencodeFuncotation checkForAndCreateSpecialAlleleFuncotation(final VariantContext variant,
                                                                     final Allele altAllele,
                                                                     final ReferenceContext reference,
                                                                     final GencodeGtfTranscriptFeature transcript) {
    // If the alt allele is a spanning deletion or a symbolic allele, create an unknown funcotation:
    if (altAllele.isSymbolic() || altAllele.equals(Allele.SPAN_DEL) ) {
        return createFuncotationForSymbolicAltAllele(variant, altAllele, transcript, reference);
    }

    // If the reference allele or alternate allele contains any masked bases:
    if ( variant.getReference().getBaseString().contains(FuncotatorConstants.MASKED_ANY_BASE_STRING) || altAllele.getBaseString().contains(FuncotatorConstants.MASKED_ANY_BASE_STRING) ) {
        return createFuncotationForMaskedBases(variant, altAllele, transcript, reference);
    }

    return null;
}

Source File: VariantEval.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

private EvalCompMatchType doEvalAndCompMatch(final VariantContext eval, final VariantContext comp, boolean requireStrictAlleleMatch) {
    if ( comp.getType() == VariantContext.Type.NO_VARIATION || eval.getType() == VariantContext.Type.NO_VARIATION )
        // if either of these are NO_VARIATION they are LENIENT matches
        return EvalCompMatchType.LENIENT;

    if ( comp.getType() != eval.getType() )
        return EvalCompMatchType.NO_MATCH;

    // find the comp which matches both the reference allele and alternate allele from eval
    final Allele altEval = eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
    final Allele altComp = comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
    if ((altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp) && eval.getReference().equals(comp.getReference())))
        return EvalCompMatchType.STRICT;
    else
        return requireStrictAlleleMatch ? EvalCompMatchType.NO_MATCH : EvalCompMatchType.LENIENT;
}

Source File: StrandBiasUtils.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

/**
 * Add another read to the strand count table
 * @param bestAllele    the Allele best supported by {@param read}
 * @param read  read to add
 * @param ref   reference Allele
 * @param allAlts   the (subset of) alternate alleles for the associated variant
 * @param perAlleleValues updated to return the values including @{value read}
 */
private static void updateTable(final Allele bestAllele, final GATKRead read, final Allele ref, final List<Allele> allAlts, final ReducibleAnnotationData<List<Integer>> perAlleleValues) {

    final boolean matchesRef = bestAllele.equals(ref, true);
    final boolean matchesAnyAlt = allAlts.contains(bestAllele);

    //can happen if a read's most likely allele has been removed when --max_alternate_alleles is exceeded
    if (!( matchesRef || matchesAnyAlt )) {
        return;
    }

    final List<Integer> alleleStrandCounts;
    if (perAlleleValues.hasAttribute(bestAllele) && perAlleleValues.getAttribute(bestAllele) != null) {
        alleleStrandCounts = perAlleleValues.getAttribute(bestAllele);
    } else {
        alleleStrandCounts = new ArrayList<>();
        alleleStrandCounts.add(0,0);
        alleleStrandCounts.add(1,0);
    }

    final int strand = read.isReverseStrand() ? REVERSE : FORWARD;
    alleleStrandCounts.set(strand, alleleStrandCounts.get(strand) + 1);
    perAlleleValues.putAttribute(bestAllele, alleleStrandCounts);
}

Source File: LiftoverUtils.java From picard with MIT License

5 votes

private static Allele reverseComplement(final Allele oldAllele) {
    if (oldAllele.isSymbolic() || oldAllele.isNoCall() || oldAllele.equals(Allele.SPAN_DEL)) {
        return oldAllele;
    } else {
        return Allele.create(SequenceUtil.reverseComplement(oldAllele.getBaseString()), oldAllele.isReference());
    }
}

Source File: HaplotypeCallerIntegrationTest.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

/**
 * Helper method for testMaxAlternateAlleles
 *
 * @param vc VariantContext to check
 * @return number of alt alleles in vc, excluding NON_REF (if present)
 */
private int getNumAltAllelesExcludingNonRef( final VariantContext vc ) {
    final List<Allele> altAlleles = vc.getAlternateAlleles();
    int numAltAllelesExcludingNonRef = 0;

    for ( final Allele altAllele : altAlleles ) {
        if ( ! altAllele.equals(Allele.NON_REF_ALLELE) ) {
            ++numAltAllelesExcludingNonRef;
        }
    }

    return numAltAllelesExcludingNonRef;
}

Source File: GencodeFuncotationFactory.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

/**
 * Creates a {@link GencodeFuncotation}s based on the given {@link Allele} with type
 * {@link GencodeFuncotation.VariantClassification#FIVE_PRIME_FLANK} or
 * {@link GencodeFuncotation.VariantClassification#THREE_PRIME_FLANK}
 *
 * @param variant The {@link VariantContext} associated with this annotation.
 * @param altAllele The alternate {@link Allele} to use for this {@link GencodeFuncotation}.
 * @param transcript {@link GencodeGtfTranscriptFeature} associated with this flank funcotation.
 * @param reference The {@link ReferenceContext} in which the given {@link Allele}s appear.
 * @param flankType {@link GencodeFuncotation.VariantClassification#FIVE_PRIME_FLANK} or
 *                  {@link GencodeFuncotation.VariantClassification#THREE_PRIME_FLANK}
 * @return A flank funcotation for the given allele
 */
private GencodeFuncotation createFlankFuncotation(final VariantContext variant, final Allele altAllele, final GencodeGtfTranscriptFeature transcript, final ReferenceContext reference, final GencodeFuncotation.VariantClassification flankType) {

    // Create a symbolic allele funcotation for the flank type, if appropriate:
    if (altAllele.isSymbolic() || altAllele.equals(Allele.SPAN_DEL) ) {
        return createFuncotationForSymbolicAltAllele(variant, altAllele, transcript, reference, flankType);
    }

    final GencodeFuncotationBuilder funcotationBuilder = new GencodeFuncotationBuilder();

    // NOTE: The reference context is ALWAYS from the + strand
    final StrandCorrectedReferenceBases referenceBases = FuncotatorUtils.createReferenceSnippet(variant.getReference(), altAllele, reference, Strand.POSITIVE, referenceWindow);
    final String referenceBasesString = referenceBases.getBaseString(Strand.POSITIVE);

    final double gcContent = calculateGcContent(variant.getReference(), altAllele, reference, gcContentWindowSizeBases);

    funcotationBuilder.setHugoSymbol(transcript.getGeneName())
            .setChromosome(variant.getContig())
            .setStart(variant.getStart())
            .setEnd(variant.getEnd())
            .setStrand(transcript.getGenomicStrand())
            .setVariantClassification(flankType)
            .setVariantType(getVariantType(variant.getReference(), altAllele))
            .setRefAllele(variant.getReference())
            .setTumorSeqAllele2(altAllele.getBaseString())
            .setGenomeChange(getGenomeChangeString(variant, altAllele))
            .setAnnotationTranscript(transcript.getTranscriptId())
            .setReferenceContext(referenceBasesString)
            .setGcContent(gcContent)
            .setNcbiBuild(ncbiBuildVersion)
            .setGeneTranscriptType(transcript.getTranscriptType());

    // Set our version:
    funcotationBuilder.setVersion(version);

    // Set our data source name:
    funcotationBuilder.setDataSourceName(getName());

    return funcotationBuilder.build();
}

Source File: GencodeFuncotationFactory.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

/**
 * Creates a {@link GencodeFuncotation}s based on the given {@link Allele} with type
 * {@link GencodeFuncotation.VariantClassification#IGR}.
 * Reports reference bases as if they are on the {@link Strand#POSITIVE} strand.
 * @param variant The {@link VariantContext} associated with this annotation.
 * @param altAllele The alternate {@link Allele} to use for this {@link GencodeFuncotation}.
 * @param reference The {@link ReferenceContext} in which the given {@link Allele}s appear.
 * @return An IGR funcotation for the given allele.
 */
private GencodeFuncotation createIgrFuncotation(final VariantContext variant,
                                                final Allele altAllele,
                                                final ReferenceContext reference){

    final GencodeFuncotationBuilder funcotationBuilder = new GencodeFuncotationBuilder();

    // Get GC Content:
    funcotationBuilder.setGcContent( calculateGcContent( variant.getReference(), altAllele, reference, gcContentWindowSizeBases ) );

    final String alleleString = altAllele.getBaseString().isEmpty() ? altAllele.toString() : altAllele.getBaseString();

    funcotationBuilder.setVariantClassification( GencodeFuncotation.VariantClassification.IGR )
                      .setRefAllele( variant.getReference() )
                      .setTumorSeqAllele2( alleleString )
                      .setStart(variant.getStart())
                      .setEnd(variant.getEnd())
                      .setVariantType(getVariantType(variant.getReference(), altAllele))
                      .setChromosome(variant.getContig())
                      .setAnnotationTranscript(FuncotationMap.NO_TRANSCRIPT_AVAILABLE_KEY);

    if ( (!altAllele.isSymbolic()) && (!altAllele.equals(Allele.SPAN_DEL)) ) {
        funcotationBuilder.setGenomeChange(getGenomeChangeString(variant, altAllele));
    }

    funcotationBuilder.setNcbiBuild(ncbiBuildVersion);

    // Set our reference context in the the FuncotatonBuilder:
    funcotationBuilder.setReferenceContext(FuncotatorUtils.createReferenceSnippet(variant.getReference(), altAllele, reference, Strand.POSITIVE, referenceWindow).getBaseString());

    // Set our version:
    funcotationBuilder.setVersion(version);

    // Set our data source name:
    funcotationBuilder.setDataSourceName(getName());

    return funcotationBuilder.build();
}

Source File: AS_FisherStrand.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

@Override
protected Map<Allele,Double> calculateReducedData(AlleleSpecificAnnotationData<List<Integer>> combinedData) {
    final Map<Allele,Double> annotationMap = new HashMap<>();
    final Map<Allele,List<Integer>> perAlleleData = combinedData.getAttributeMap();
    final List<Integer> refStrandCounts = perAlleleData.get(combinedData.getRefAllele());
    for (final Allele a : perAlleleData.keySet()) {
        if(!a.equals(combinedData.getRefAllele(),true)) {
            final List<Integer> altStrandCounts = combinedData.getAttribute(a);
            final int[][] refAltTable = new int[][]{new int[]{refStrandCounts.get(0), refStrandCounts.get(1)}, new int[]{altStrandCounts.get(0), altStrandCounts.get(1)}};
            annotationMap.put(a, QualityUtils.phredScaleErrorRate(Math.max(FisherStrand.pValueForContingencyTable(refAltTable), MIN_PVALUE)));
        }
    }
    return annotationMap;
}

Source File: AS_RankSumTest.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

public Map<Allele, Double> calculateReducedData(final Map<Allele, Histogram> perAlleleValues, final Allele ref) {
    final Map<Allele, Double> perAltRankSumResults = new HashMap<>();
    for (final Allele alt : perAlleleValues.keySet()) {
        if (!alt.equals(ref, false) && perAlleleValues.get(alt) != null) {
            perAltRankSumResults.put(alt, perAlleleValues.get(alt).median());
        }
    }
    return perAltRankSumResults;
}

Source File: StrandBiasTest.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

private static void updateTable(final int[] table, final Allele allele, final GATKRead read, final Allele ref, final List<Allele> allAlts) {
    final boolean matchesRef = allele.equals(ref, true);
    final boolean matchesAnyAlt = allAlts.contains(allele);

    if ( matchesRef || matchesAnyAlt ) {
        final int offset = matchesRef ? 0 : ARRAY_DIM;

        // a normal read with an actual strand
        final boolean isForward = !read.isReverseStrand();
        table[offset + (isForward ? 0 : 1)]++;
    }
}

Source File: ApplyVQSR.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

private VariantContext getMatchingRecalVC(final VariantContext target, final List<VariantContext> recalVCs, final Allele allele) {
    for( final VariantContext recalVC : recalVCs ) {
        if ( target.getEnd() == recalVC.getEnd() ) {
            if (!useASannotations)
                return recalVC;
            else if (allele.equals(recalVC.getAlternateAllele(0)))
                return recalVC;
        }
    }
    return null;
}

Source File: GenotypeConcordanceTest.java From picard with MIT License

5 votes

/**
 * Simple method to return a list of unique alleles.
 */
private List<Allele> makeUniqueListOfAlleles(final Allele... alleles) {
    final Set<Allele> uniqueAlleles = new HashSet<Allele>();
    for (final Allele allele : alleles) {
        if (!allele.equals(Allele.NO_CALL)) {
            uniqueAlleles.add(allele);
        }
    }
    if (!uniqueAlleles.contains(Aref)) uniqueAlleles.add(Aref);
    return new ArrayList<Allele>(uniqueAlleles);
}

Source File: SelectVariants.java From gatk with BSD 3-Clause "New" or "Revised" License

4 votes

private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC, final Set<String> selectedSampleNames) {
    if (fullyDecode) {
        return; // TODO -- annotations are broken with fully decoded data
    }

    if (keepOriginalChrCounts) {
        final int[] indexOfOriginalAlleleForNewAllele;
        final List<Allele> newAlleles = builder.getAlleles();
        final int numOriginalAlleles = originalVC.getNAlleles();

        // if the alleles already match up, we can just copy the previous list of counts
        if (numOriginalAlleles == newAlleles.size()) {
            indexOfOriginalAlleleForNewAllele = null;
        }
        // otherwise we need to parse them and select out the correct ones
        else {
            indexOfOriginalAlleleForNewAllele = new int[newAlleles.size() - 1];
            Arrays.fill(indexOfOriginalAlleleForNewAllele, -1);

            // note that we don't care about the reference allele at position 0
            for (int newI = 1; newI < newAlleles.size(); newI++) {
                final Allele newAlt = newAlleles.get(newI);
                for (int oldI = 0; oldI < numOriginalAlleles - 1; oldI++) {
                    if (newAlt.equals(originalVC.getAlternateAllele(oldI), false)) {
                        indexOfOriginalAlleleForNewAllele[newI - 1] = oldI;
                        break;
                    }
                }
            }
        }

        if (originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AC_KEY,
                    getReorderedAttributes(originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY), indexOfOriginalAlleleForNewAllele));
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AF_KEY,
                    getReorderedAttributes(originalVC.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY), indexOfOriginalAlleleForNewAllele));
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AN_KEY, originalVC.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
        }
    }

    VariantContextUtils.calculateChromosomeCounts(builder, false);

    if (keepOriginalDepth && originalVC.hasAttribute(VCFConstants.DEPTH_KEY)) {
        builder.attribute(GATKVCFConstants.ORIGINAL_DP_KEY, originalVC.getAttribute(VCFConstants.DEPTH_KEY));
    }

    boolean sawDP = false;
    int depth = 0;
    for (final String sample : selectedSampleNames ) {
        final Genotype g = originalVC.getGenotype(sample);
        if (!g.isFiltered()) {
            if (g.hasDP()) {
                depth += g.getDP();
                sawDP = true;
            }
        }
    }

    if (sawDP) {
        builder.attribute(VCFConstants.DEPTH_KEY, depth);
    }
}

Source File: GATKVCFConstants.java From gatk with BSD 3-Clause "New" or "Revised" License

4 votes

public static boolean isSpanningDeletion(final Allele allele){
    return allele.equals(Allele.SPAN_DEL) || allele.equals(SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED);
}

Source File: GtcToVcf.java From picard with MIT License

4 votes

private VariantContext makeVariantContext(Build37ExtendedIlluminaManifestRecord record, final InfiniumGTCRecord gtcRecord,
                                          final InfiniumEGTFile egtFile, final ProgressLogger progressLogger) {
    // If the record is not flagged as errant in the manifest we include it in the VCF
    Allele A = record.getAlleleA();
    Allele B = record.getAlleleB();
    Allele ref = record.getRefAllele();

    final String chr = record.getB37Chr();
    final Integer position = record.getB37Pos();
    final Integer endPosition = position + ref.length() - 1;
    Integer egtIndex = egtFile.rsNameToIndex.get(record.getName());
    if (egtIndex == null) {
        throw new PicardException("Found no record in cluster file for manifest entry '" + record.getName() + "'");
    }

    progressLogger.record(chr, position);

    // Create list of unique alleles
    final List<Allele> assayAlleles = new ArrayList<>();
    assayAlleles.add(ref);

    if (A.equals(B)) {
        throw new PicardException("Found same allele (" + A.getDisplayString() + ") for A and B ");
    }

    if (!ref.equals(A, true)) {
        assayAlleles.add(A);
    }

    if (!ref.equals(B, true)) {
        assayAlleles.add(B);
    }

    final String sampleName = FilenameUtils.removeExtension(INPUT.getName());
    final Genotype genotype = getGenotype(sampleName, gtcRecord, record, A, B);

    final VariantContextBuilder builder = new VariantContextBuilder();

    builder.source(record.getName());
    builder.chr(chr);
    builder.start(position);
    builder.stop(endPosition);
    builder.alleles(assayAlleles);
    builder.log10PError(VariantContext.NO_LOG10_PERROR);
    builder.id(record.getName());
    builder.genotypes(genotype);

    VariantContextUtils.calculateChromosomeCounts(builder, false);

    //custom info fields
    builder.attribute(InfiniumVcfFields.ALLELE_A, record.getAlleleA());
    builder.attribute(InfiniumVcfFields.ALLELE_B, record.getAlleleB());
    builder.attribute(InfiniumVcfFields.ILLUMINA_STRAND, record.getIlmnStrand());
    builder.attribute(InfiniumVcfFields.PROBE_A, record.getAlleleAProbeSeq());
    builder.attribute(InfiniumVcfFields.PROBE_B, record.getAlleleBProbeSeq());
    builder.attribute(InfiniumVcfFields.BEADSET_ID, record.getBeadSetId());
    builder.attribute(InfiniumVcfFields.ILLUMINA_CHR, record.getChr());
    builder.attribute(InfiniumVcfFields.ILLUMINA_POS, record.getPosition());
    builder.attribute(InfiniumVcfFields.ILLUMINA_BUILD, record.getGenomeBuild());
    builder.attribute(InfiniumVcfFields.SOURCE, record.getSource().replace(' ', '_'));
    builder.attribute(InfiniumVcfFields.GC_SCORE, formatFloatForVcf(egtFile.totalScore[egtIndex]));

    for (InfiniumVcfFields.GENOTYPE_VALUES gtValue : InfiniumVcfFields.GENOTYPE_VALUES.values()) {
        final int ordinalValue = gtValue.ordinal();
        builder.attribute(InfiniumVcfFields.N[ordinalValue], egtFile.n[egtIndex][ordinalValue]);
        builder.attribute(InfiniumVcfFields.DEV_R[ordinalValue], formatFloatForVcf(egtFile.devR[egtIndex][ordinalValue]));
        builder.attribute(InfiniumVcfFields.MEAN_R[ordinalValue], formatFloatForVcf(egtFile.meanR[egtIndex][ordinalValue]));
        builder.attribute(InfiniumVcfFields.DEV_THETA[ordinalValue], formatFloatForVcf(egtFile.devTheta[egtIndex][ordinalValue]));
        builder.attribute(InfiniumVcfFields.MEAN_THETA[ordinalValue], formatFloatForVcf(egtFile.meanTheta[egtIndex][ordinalValue]));

        final EuclideanValues genotypeEuclideanValues = polarToEuclidean(egtFile.meanR[egtIndex][ordinalValue], egtFile.devR[egtIndex][ordinalValue],
                egtFile.meanTheta[egtIndex][ordinalValue], egtFile.devTheta[egtIndex][ordinalValue]);
        builder.attribute(InfiniumVcfFields.DEV_X[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.devX));
        builder.attribute(InfiniumVcfFields.MEAN_X[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.meanX));
        builder.attribute(InfiniumVcfFields.DEV_Y[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.devY));
        builder.attribute(InfiniumVcfFields.MEAN_Y[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.meanY));
    }


    final String rsid = record.getRsId();
    if (StringUtils.isNotEmpty(rsid)) {
        builder.attribute(InfiniumVcfFields.RS_ID, rsid);
    }
    if (egtFile.totalScore[egtIndex] == 0.0) {
        builder.filter(InfiniumVcfFields.ZEROED_OUT_ASSAY);
        if (genotype.isCalled()) {
            if (DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS) {
                throw new PicardException("Found a call (genotype: " + genotype + ") on a zeroed out Assay!!");
            } else {
                log.warn("Found a call (genotype: " + genotype + ") on a zeroed out Assay. " +
                        "This could occur if you called genotypes on a different cluster file than used here.");
            }
        }
    }
    if (record.isDupe()) {
        builder.filter(InfiniumVcfFields.DUPE);
    }
    return builder.make();
}

Source File: FuncotatorIntegrationTest.java From gatk with BSD 3-Clause "New" or "Revised" License

4 votes

@Test
public void testCanAnnotateSpanningDeletions() {
    final FuncotatorArgumentDefinitions.OutputFormatType outputFormatType = FuncotatorArgumentDefinitions.OutputFormatType.VCF;
    final File outputFile = getOutputFile(outputFormatType);

    final ArgumentsBuilder arguments = createBaselineArgumentsForFuncotator(
            SPANNING_DEL_VCF,
            outputFile,
            hg38Chr3Ref,
            DS_PIK3CA_DIR,
            FuncotatorTestConstants.REFERENCE_VERSION_HG38,
            outputFormatType,
            false);

    runCommandLine(arguments);

    final Pair<VCFHeader, List<VariantContext>> vcfInfo = VariantContextTestUtils.readEntireVCFIntoMemory(outputFile.getAbsolutePath());
    final List<VariantContext> variantContexts = vcfInfo.getRight();
    Assert.assertTrue(variantContexts.size() > 0);
    final VCFHeader vcfHeader = vcfInfo.getLeft();
    final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNCOTATOR_VCF_FIELD_NAME);
    final String[] funcotationKeys = FuncotatorUtils.extractFuncotatorKeysFromHeaderDescription(funcotationHeaderLine.getDescription());

    final int NUM_VARIANTS = 10;
    Assert.assertEquals(variantContexts.size(), NUM_VARIANTS);
    Assert.assertEquals(variantContexts.stream().filter(v -> v.hasAllele(Allele.SPAN_DEL)).count(), NUM_VARIANTS);

    for (final VariantContext vc : variantContexts) {
        final Map<Allele, FuncotationMap> alleleToFuncotationMap = FuncotatorUtils.createAlleleToFuncotationMapFromFuncotationVcfAttribute(funcotationKeys,
                vc, "Gencode_28_annotationTranscript", "TEST");

        // Make sure that all spanning deletions are funcotated with could not determine and that the others are something else.
        for (final Allele allele : alleleToFuncotationMap.keySet()) {
            final List<String> txIds = alleleToFuncotationMap.get(allele).getTranscriptList();
            for (final String txId : txIds) {
                if (allele.equals(Allele.SPAN_DEL)) {
                    Assert.assertEquals(alleleToFuncotationMap.get(allele).get(txId).get(0).getField("Gencode_28_variantClassification"), GencodeFuncotation.VariantClassification.COULD_NOT_DETERMINE.toString());
                    Assert.assertEquals(alleleToFuncotationMap.get(allele).get(txId).get(0).getField("Gencode_28_variantType"), GencodeFuncotation.VariantType.NA.toString());
                } else {
                    Assert.assertNotEquals(alleleToFuncotationMap.get(allele).get(txId).get(0).getField("Gencode_28_variantClassification"), GencodeFuncotation.VariantClassification.COULD_NOT_DETERMINE.toString());
                }
            }
        }
    }
}

Java Code Examples for htsjdk.variant.variantcontext.Allele#equals()