htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder Java Examples

void write(@NotNull final PurityAdjuster purityAdjuster, @NotNull final List<PurpleCopyNumber> copyNumbers) throws IOException {
    if (header.isPresent()) {
        try (final IndexedFastaSequenceFile indexedFastaSequenceFile = new IndexedFastaSequenceFile(new File(refGenomePath));
                final VariantContextWriter writer = new VariantContextWriterBuilder().setOutputFile(outputVCF)
                        .setReferenceDictionary(header.get().getSequenceDictionary())
                        .setIndexCreator(new TabixIndexCreator(header.get().getSequenceDictionary(), new TabixFormat()))
                        .setOutputFileType(VariantContextWriterBuilder.OutputType.BLOCK_COMPRESSED_VCF)
                        .setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER)
                        .build()) {

            final StructuralRefContextEnrichment refEnricher =
                    new StructuralRefContextEnrichment(indexedFastaSequenceFile, writer::add);
            writer.writeHeader(refEnricher.enrichHeader(header.get()));

            enriched(purityAdjuster, copyNumbers).forEach(refEnricher);
            refEnricher.flush();
        }
    }
}
 

/**
 * Writes out the VariantContext objects in the order presented to the supplied output file
 * in VCF format.
 */
private void writeVcf(final SortingCollection<VariantContext> variants,
                      final File output,
                      final SAMSequenceDictionary dict,
                      final VCFHeader vcfHeader) {

    try (final VariantContextWriter writer = new VariantContextWriterBuilder()
            .setOutputFile(output)
            .setReferenceDictionary(dict)
            .setOptions(VariantContextWriterBuilder.DEFAULT_OPTIONS)
            .build()) {

        writer.writeHeader(vcfHeader);

        for (final VariantContext variant : variants) {
            if (variant.getAlternateAlleles().size() > 1) {
                variant.getCommonInfo().addFilter(InfiniumVcfFields.TRIALLELIC);
            }

            writer.add(variant);
        }
    }
}
 

/**
 * Converts a list of variants into a VCF file, given a {@link VCFHeader}
 * and an {@link OutputStream}.
 * <p> This function uses HTSJDK to create {@link VariantCall} objects then
 * writes them to the given output stream. Note that this implementation depends
 * heavily on HTSJDK and makes the same assumptions as HTSJDK (e.g. integer values GQ).
 *
 * @param header The header to use to generate the output VCF
 * @param variants A list of variants to encode in the output VCF
 * @param os The output stream to which to write the generated VCF
 */
public static void convertVariantToVcf(VCFHeader header, List<Variant> variants,
    OutputStream os, boolean writeHeader) {
  if (vcfWriter == null) {
    vcfWriter = new VariantContextWriterBuilder().clearOptions()
        .setOutputVCFStream(os).build();
  }

  if (writeHeader) {
    vcfWriter.writeHeader(header);
  }

  for (Variant currVariant : variants) {
    vcfWriter.add(getContextFromVariant(header, currVariant));
  }
}
 

private static void processVariants(boolean strelka, @NotNull final String filePath, @NotNull final String outputVcf,
        @NotNull final String tumorBam) {
    final VCFFileReader vcfReader = new VCFFileReader(new File(filePath), false);
    final VCFHeader outputHeader = generateOutputHeader(vcfReader.getFileHeader(), "TUMOR");
    final VariantContextWriter vcfWriter = new VariantContextWriterBuilder().setOutputFile(outputVcf)
            .setReferenceDictionary(vcfReader.getFileHeader().getSequenceDictionary())
            .build();
    vcfWriter.writeHeader(outputHeader);
    final MNVValidator validator = ImmutableMNVValidator.of(tumorBam);
    final MNVMerger merger = ImmutableMNVMerger.of(outputHeader);
    Pair<PotentialMNVRegion, Optional<PotentialMNVRegion>> outputPair = ImmutablePair.of(PotentialMNVRegion.empty(), Optional.empty());
    for (final VariantContext rawVariant : vcfReader) {
        final VariantContext simplifiedVariant =
                strelka ? StrelkaPostProcess.simplifyVariant(rawVariant, StrelkaPostProcess.TUMOR_GENOTYPE) : rawVariant;

        final PotentialMNVRegion potentialMNV = outputPair.getLeft();
        outputPair = MNVDetector.addMnvToRegion(potentialMNV, simplifiedVariant);
        outputPair.getRight().ifPresent(mnvRegion -> validator.mergeVariants(mnvRegion, merger).forEach(vcfWriter::add));
    }
    validator.mergeVariants(outputPair.getLeft(), merger).forEach(vcfWriter::add);
    vcfWriter.close();
    vcfReader.close();
    LOGGER.info("Written output variants to " + outputVcf);
}
 

/** Gets the variant context writer if the output VCF is to be written, otherwise empty. */
private Optional<VariantContextWriter> getVariantContextWriter(final VCFFileReader truthReader, final VCFFileReader callReader) {
    if (OUTPUT_VCF) {
        final File outputVcfFile = new File(OUTPUT + OUTPUT_VCF_FILE_EXTENSION);
        final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
                .setOutputFile(outputVcfFile)
                .setReferenceDictionary(callReader.getFileHeader().getSequenceDictionary())
                .setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER)
                .setOption(Options.INDEX_ON_THE_FLY);
        final VariantContextWriter writer = builder.build();

        // create the output header
        final List<String> sampleNames = Arrays.asList(OUTPUT_VCF_CALL_SAMPLE_NAME, OUTPUT_VCF_TRUTH_SAMPLE_NAME);
        final Set<VCFHeaderLine> headerLines = new HashSet<>();
        headerLines.addAll(callReader.getFileHeader().getMetaDataInInputOrder());
        headerLines.addAll(truthReader.getFileHeader().getMetaDataInInputOrder());
        headerLines.add(CONTINGENCY_STATE_HEADER_LINE);
        writer.writeHeader(new VCFHeader(headerLines, sampleNames));
        return Optional.of(writer);
    }
    else {
        return Optional.empty();
    }
}
 

public void writeBAF(@NotNull final String filename, @NotNull final Collection<TumorBAF> tumorEvidence,  @NotNull final AmberHetNormalEvidence hetNormalEvidence) {
    final List<TumorBAF> list = Lists.newArrayList(tumorEvidence);
    Collections.sort(list);

    final VariantContextWriter writer =
            new VariantContextWriterBuilder().setOutputFile(filename).modifyOption(Options.INDEX_ON_THE_FLY, true).build();
    final VCFHeader header = header(config.tumorOnly() ? Collections.singletonList(config.tumor()) : config.allSamples());
    writer.setHeader(header);
    writer.writeHeader(header);

    final ListMultimap<AmberSite, Genotype> genotypeMap = ArrayListMultimap.create();
    for (final String sample : hetNormalEvidence.samples()) {
        for (BaseDepth baseDepth : hetNormalEvidence.evidence(sample)) {
            genotypeMap.put(AmberSiteFactory.asSite(baseDepth), createGenotype(sample, baseDepth));
        }
    }

    for (final TumorBAF tumorBAF : list) {
        AmberSite tumorSite = AmberSiteFactory.tumorSite(tumorBAF);
        genotypeMap.put(tumorSite, createGenotype(tumorBAF));
        writer.add(create(tumorBAF, genotypeMap.get(tumorSite)));
    }

    writer.close();
}
 

private static VariantContextWriter getVariantContextWriter(final File outputFile,
                                                            final File referenceSequenceFileName,
                                                            final String sample,
                                                            final String source,
                                                            final ReferenceSequenceFile ref) {
    final VariantContextWriter variantContextWriter = new VariantContextWriterBuilder()
            .setReferenceDictionary(ref.getSequenceDictionary())
            .setOutputFile(outputFile).build();

    final Set<VCFHeaderLine> lines = new LinkedHashSet<>();
    lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath()));
    lines.add(new VCFHeaderLine("source", source));
    lines.add(new VCFHeaderLine("fileDate", new Date().toString()));

    lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_PL_KEY));
    lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS));
    lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY));

    final VCFHeader header = new VCFHeader(lines, Collections.singletonList(sample));
    header.setSequenceDictionary(ref.getSequenceDictionary());
    variantContextWriter.writeHeader(header);
    return variantContextWriter;
}
 

private AnnotateStrelkaWithAllelicDepth(final Options options, final String... args) throws ParseException {
    final CommandLine cmd = createCommandLine(args, options);
    if (!cmd.hasOption(VCF_IN)) {
        throw new ParseException(VCF_IN + " is a mandatory argument");
    }

    if (!cmd.hasOption(VCF_OUT)) {
        throw new ParseException(VCF_OUT + " is a mandatory argument");
    }

    inputVCF = cmd.getOptionValue(VCF_IN);
    outputVCF = cmd.getOptionValue(VCF_OUT);

    vcfReader = new VCFFileReader(new File(inputVCF), false);
    header = generateOutputHeader(vcfReader.getFileHeader());
    vcfWriter = new VariantContextWriterBuilder().setOutputFile(outputVCF)
            .setReferenceDictionary(header.getSequenceDictionary())
            .setIndexCreator(new TabixIndexCreator(header.getSequenceDictionary(), new TabixFormat()))
            .setOption(htsjdk.variant.variantcontext.writer.Options.ALLOW_MISSING_FIELDS_IN_HEADER)
            .build();
}
 

public void writeAsVcf(final File output, final File refFile) throws FileNotFoundException {
    ReferenceSequenceFile ref = new IndexedFastaSequenceFile(refFile);
    try (VariantContextWriter writer = new VariantContextWriterBuilder()
            .setOutputFile(output)
            .setReferenceDictionary(ref.getSequenceDictionary())
            .build()) {

        final VCFHeader vcfHeader = new VCFHeader(
                VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false),
                Collections.singleton(HET_GENOTYPE_FOR_PHASING));

        VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false);

        vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString()));
        vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"));
        vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
        vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.String, "Phase-set identifier for phased genotypes."));
        vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeader.SOURCE_KEY,"HaplotypeMap::writeAsVcf"));
        vcfHeader.addMetaDataLine(new VCFHeaderLine("reference","HaplotypeMap::writeAsVcf"));


      //  vcfHeader.addMetaDataLine(new VCFHeaderLine());
        writer.writeHeader(vcfHeader);
        final LinkedList<VariantContext> variants = new LinkedList<>(this.asVcf(ref));
        variants.sort(vcfHeader.getVCFRecordComparator());
        variants.forEach(writer::add);
    }
}
 

@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
    IOUtil.assertFileIsWritable(OUTPUT);

    final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY.toPath());

    final VCFFileReader fileReader = new VCFFileReader(INPUT, false);
    final VCFHeader fileHeader = fileReader.getFileHeader();

    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setReferenceDictionary(samSequenceDictionary)
            .clearOptions();
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);

    final VariantContextWriter vcfWriter = builder.setOutputFile(OUTPUT).build();
    fileHeader.setSequenceDictionary(samSequenceDictionary);
    vcfWriter.writeHeader(fileHeader);

    final ProgressLogger progress = new ProgressLogger(log, 10000);
    final CloseableIterator<VariantContext> iterator = fileReader.iterator();
    while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
        vcfWriter.add(context);
        progress.record(context.getContig(), context.getStart());
    }

    CloserUtil.close(iterator);
    CloserUtil.close(fileReader);
    vcfWriter.close();

    return 0;
}
 

@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    final VCFFileReader in = new VCFFileReader(INPUT, false);
    final VCFHeader header = in.getFileHeader();

    if (header.getGenotypeSamples().size() > 1) {
        throw new IllegalArgumentException("Input VCF must be single-sample.");
    }

    if (OLD_SAMPLE_NAME != null && !OLD_SAMPLE_NAME.equals(header.getGenotypeSamples().get(0))) {
        throw new IllegalArgumentException("Input VCF did not contain expected sample. Contained: " + header.getGenotypeSamples().get(0));
    }

    final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
    if (CREATE_INDEX) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);

    final VCFHeader outHeader = new VCFHeader(header.getMetaDataInInputOrder(), CollectionUtil.makeList(NEW_SAMPLE_NAME));
    final VariantContextWriter out = new VariantContextWriterBuilder()
            .setOptions(options)
            .setOutputFile(OUTPUT).setReferenceDictionary(outHeader.getSequenceDictionary()).build();
    out.writeHeader(outHeader);

    for (final VariantContext ctx : in) {
        out.add(ctx);
    }

    out.close();
    in.close();

    return 0;
}
 

private void writeSortedOutput(final VCFHeader outputHeader, final SortingCollection<VariantContext> sortedOutput) {
    final ProgressLogger writeProgress = new ProgressLogger(log, 25000, "wrote", "records");
    final EnumSet<Options> options = CREATE_INDEX ? EnumSet.of(Options.INDEX_ON_THE_FLY) : EnumSet.noneOf(Options.class);
    final VariantContextWriter out = new VariantContextWriterBuilder().
            setReferenceDictionary(outputHeader.getSequenceDictionary()).
            setOptions(options).
            setOutputFile(OUTPUT).build();
    out.writeHeader(outputHeader);
    for (final VariantContext variantContext : sortedOutput) {
        out.add(variantContext);
        writeProgress.record(variantContext.getContig(), variantContext.getStart());
    }
    out.close();
}
 

private void writeAllViolations(final MendelianViolationDetector.Result result) {
    if (VCF_DIR != null) {
        LOG.info(String.format("Writing family violation VCFs to %s/", VCF_DIR.getAbsolutePath()));

        final VariantContextComparator vcComparator = new VariantContextComparator(inputHeader.get().getContigLines());
        final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>(inputHeader.get().getMetaDataInInputOrder());

        headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.MENDELIAN_VIOLATION_KEY, 1, VCFHeaderLineType.String, "Type of mendelian violation."));
        headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AC, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC"));
        headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AF, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF"));
        headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AN, 1, VCFHeaderLineType.Integer, "Original AN"));

        for (final PedFile.PedTrio trio : pedFile.get().values()) {
            final File outputFile = new File(VCF_DIR, IOUtil.makeFileNameSafe(trio.getFamilyId() + IOUtil.VCF_FILE_EXTENSION));
            LOG.info(String.format("Writing %s violation VCF to %s", trio.getFamilyId(), outputFile.getAbsolutePath()));

            final VariantContextWriter out = new VariantContextWriterBuilder()
                    .setOutputFile(outputFile)
                    .unsetOption(INDEX_ON_THE_FLY)
                    .build();

            final VCFHeader newHeader = new VCFHeader(headerLines, CollectionUtil.makeList(trio.getMaternalId(), trio.getPaternalId(), trio.getIndividualId()));
            final TreeSet<VariantContext> orderedViolations = new TreeSet<>(vcComparator);

            orderedViolations.addAll(result.violations().get(trio.getFamilyId()));
            out.writeHeader(newHeader);
            orderedViolations.forEach(out::add);

            out.close();
        }
    }
}
 

@Override
protected int doWork() {
    final ProgressLogger progress = new ProgressLogger(LOG, 10000);
    
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    final VCFFileReader reader = new VCFFileReader(INPUT, REQUIRE_INDEX);
    final VCFHeader header = new VCFHeader(reader.getFileHeader());
    final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();
    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available in the input file when creating indexed output.");
    }

    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setOutputFile(OUTPUT)
            .setReferenceDictionary(sequenceDictionary);
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);
    else
        builder.unsetOption(Options.INDEX_ON_THE_FLY);
    final VariantContextWriter writer = builder.build();
    writer.writeHeader(header);
    final CloseableIterator<VariantContext> iterator = reader.iterator();

    while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
        writer.add(context);
        progress.record(context.getContig(), context.getStart());
    }

    CloserUtil.close(iterator);
    CloserUtil.close(reader);
    writer.close();

    return 0;
}
 

/**
 * This method makes a copy of the input VCF and creates an index file for it in the same location.
 * This is done so that we don't need to store the index file in the same repo
 * The copy of the input is done so that it and its index are in the same directory which is typically required.
 *
 * @param vcfFile the vcf file to index
 * @return File a vcf file (index file is created in same path).
 */
public static File createTemporaryIndexedVcfFromInput(final File vcfFile, final String tempFilePrefix, final String suffix) throws IOException {
    final String extension;

    if (suffix != null) {
        extension = suffix;
    } else if (vcfFile.getAbsolutePath().endsWith(".vcf")) {
        extension = ".vcf";
    } else if (vcfFile.getAbsolutePath().endsWith(".vcf.gz")) {
        extension = ".vcf.gz";
    } else {
        extension = "";
    }

    if (!extension.equals(".vcf") && !extension.equals(".vcf.gz")) {
        throw new IllegalArgumentException("couldn't find a .vcf or .vcf.gz ending for input file " + vcfFile.getAbsolutePath());
    }

    File output = createTemporaryIndexedFile(tempFilePrefix, extension);

    try (final VCFFileReader in = new VCFFileReader(vcfFile, false)) {
        final VCFHeader header = in.getFileHeader();
        try (final VariantContextWriter out = new VariantContextWriterBuilder().
                setReferenceDictionary(header.getSequenceDictionary()).
                setOptions(EnumSet.of(Options.INDEX_ON_THE_FLY)).
                setOutputFile(output).build()) {
            out.writeHeader(header);
            for (final VariantContext ctx : in) {
                out.add(ctx);
            }
        }
    }
    return output;
}
 

/**
 * Creates a VariantContextWriter whose outputFile type is based on the extension of the output file name.
 * The default options set by VariantContextWriter are cleared before applying ALLOW_MISSING_FIELDS_IN_HEADER (if
 * <code>lenientProcessing</code> is set), followed by the set of options specified by any <code>options</code> args.
 *
 * @param outPath output Path for this writer. May not be null.
 * @param referenceDictionary required if on the fly indexing is set, otherwise can be null
 * @param createMD5 true if an md5 file should be created
 * @param options variable length list of additional Options to be set for this writer
 * @returns VariantContextWriter must be closed by the caller
 */
public static VariantContextWriter createVCFWriter(
        final Path outPath,
        final SAMSequenceDictionary referenceDictionary,
        final boolean createMD5,
        final Options... options)
{
    Utils.nonNull(outPath);

    VariantContextWriterBuilder vcWriterBuilder =
            new VariantContextWriterBuilder().clearOptions().setOutputPath(outPath);

    if (VariantContextWriterBuilder.OutputType.UNSPECIFIED == VariantContextWriterBuilder.determineOutputTypeFromFile(outPath)) {
        // the only way the user has to specify an output type is by file extension, and htsjdk
        // throws if it can't map the file extension to a known vcf type, so fallback to a default
        // of VCF
        logger.warn(String.format(
                "Can't determine output variant file format from output file extension \"%s\". Defaulting to VCF.",
                FilenameUtils.getExtension(outPath.getFileName().toString())));
        vcWriterBuilder = vcWriterBuilder.setOutputFileType(VariantContextWriterBuilder.OutputType.VCF);
    }

    if (createMD5) {
        vcWriterBuilder.setCreateMD5();
    }

    if (null != referenceDictionary) {
        vcWriterBuilder = vcWriterBuilder.setReferenceDictionary(referenceDictionary);
    }

    for (Options opt : options) {
        vcWriterBuilder = vcWriterBuilder.setOption(opt);
    }

    return vcWriterBuilder.build();
}
 

private static VariantContextWriter getVariantContextWriter(final OutputStream outputStream,
                                                            final SAMSequenceDictionary referenceSequenceDictionary) {
    VariantContextWriterBuilder vcWriterBuilder = new VariantContextWriterBuilder()
            .clearOptions()
            .setOutputStream(outputStream);

    if (null != referenceSequenceDictionary) {
        vcWriterBuilder = vcWriterBuilder.setReferenceDictionary(referenceSequenceDictionary);
    }
    for (final Options opt : new Options[]{}) {
        vcWriterBuilder = vcWriterBuilder.setOption(opt);
    }

    return vcWriterBuilder.build();
}
 

private VariantContextWriter openVCFWriter(final File outputFile, final Set<String> samples) {
    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder();
    builder.setOutputFile(outputFile);
    builder.clearOptions();
    final VariantContextWriter result = builder.build();
    final VCFHeader header = new VCFHeader(Collections.emptySet(), samples);
    CopyNumberTriStateAllele.addHeaderLinesTo(header);
    EvaluationClass.addHeaderLinesTo(header);

    // Format annotations.
    header.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.Character, "Called genotype"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALL_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Quality of the call"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALLED_SEGMENTS_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of called segments that overlap with the truth"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALLED_ALLELE_COUNTS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Called allele count for mixed calls"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.TRUTH_COPY_FRACTION_KEY, 1, VCFHeaderLineType.Float, "Truth copy fraction estimated"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.TRUTH_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Truth call quality"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.EVALUATION_CLASS_KEY, 1, VCFHeaderLineType.Character, "The evaluation class for the call or lack of call. It the values of the header key '" + EvaluationClass.VCF_HEADER_KEY + "'"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.TRUTH_GENOTYPE_KEY, 1, VCFHeaderLineType.Character, "The truth genotype"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALLED_TARGET_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of targets covered by called segments"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALL_QUALITY_KEY, 1, VCFHeaderLineType.Float, "1 - The probability of th event in Phred scale (the maximum if ther are more than one segment"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "The quality of the call (the maximum if there are more than one segment"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Character, "Genotype filters"));

    // Info annotations.
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.TRUTH_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "The frequency of the alternative alleles in the truth callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.TRUTH_ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of called alleles in the truth callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.CALLS_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "The frequency of the alternative alleles in the actual callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.CALLS_ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of called alleles in the actual callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.TRUTH_TARGET_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of targets overlapped by this variant"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position for the variant"));

    // Filter annotations.
    for (final EvaluationFilter filter : EvaluationFilter.values()) {
        header.addMetaDataLine(new VCFFilterHeaderLine(filter.name(), filter.description));
        header.addMetaDataLine(new VCFFilterHeaderLine(filter.acronym, filter.description));
    }
    header.addMetaDataLine(new VCFFilterHeaderLine(EvaluationFilter.PASS, "Indicates that it passes all filters"));
    result.writeHeader(header);
    return result;
}
 

public void write(@NotNull final String filename, @NotNull final List<HotspotEvidence> evidenceList) {
    final VariantContextWriter writer =
            new VariantContextWriterBuilder().setOutputFile(filename).modifyOption(Options.INDEX_ON_THE_FLY, false).build();
    writer.setHeader(header);
    writer.writeHeader(header);

    final ListMultimap<GenomePosition, HotspotEvidence> evidenceMap = Multimaps.index(evidenceList, GenomePositions::create);
    for (GenomePosition site : evidenceMap.keySet()) {
        final List<HotspotEvidence> evidence = evidenceMap.get(site);
        final VariantContext context = create(evidence);
        writer.add(context);
    }

    writer.close();
}
 

void writeContamination(@NotNull final String filename, @NotNull final Collection<TumorContamination> evidence) {
    final List<TumorContamination> list = Lists.newArrayList(evidence);
    Collections.sort(list);

    final VariantContextWriter writer =
            new VariantContextWriterBuilder().setOutputFile(filename).modifyOption(Options.INDEX_ON_THE_FLY, true).build();
    final VCFHeader header = header(Lists.newArrayList(config.primaryReference(), config.tumor()));
    writer.setHeader(header);
    writer.writeHeader(header);

    list.forEach(x -> writer.add(create(x)));
    writer.close();
}
 

void writeSNPCheck(@NotNull final String filename, @NotNull final List<BaseDepth> baseDepths) {
    final List<BaseDepth> list = Lists.newArrayList(baseDepths);
    Collections.sort(list);

    final VariantContextWriter writer =
            new VariantContextWriterBuilder().setOutputFile(filename).modifyOption(Options.INDEX_ON_THE_FLY, true).build();
    final VCFHeader header = header(Lists.newArrayList(config.primaryReference()));
    writer.setHeader(header);
    writer.writeHeader(header);

    list.forEach(x -> writer.add(create(x)));
    writer.close();
}
 

public SageVCF(@NotNull final IndexedFastaSequenceFile reference, @NotNull final SageConfig config) {
    writer = new VariantContextWriterBuilder().setOutputFile(config.outputFile())
            .modifyOption(Options.INDEX_ON_THE_FLY, true)
            .modifyOption(Options.USE_ASYNC_IO, false)
            .setReferenceDictionary(reference.getSequenceDictionary())
            .build();
    refContextEnrichment = new SomaticRefContextEnrichment(reference, this::writeToFile);

    final VCFHeader header = refContextEnrichment.enrichHeader(header(config));
    header.setSequenceDictionary(reference.getSequenceDictionary());
    writer.writeHeader(header);
}
 

PonVCF(final String output, int sampleSize) {
    writer = new VariantContextWriterBuilder().setOutputFile(output)
            .modifyOption(Options.INDEX_ON_THE_FLY, false)
            .modifyOption(Options.USE_ASYNC_IO, false)
            .modifyOption(Options.DO_NOT_WRITE_GENOTYPES, true)
            .build();

    final VCFHeader header = new VCFHeader();
    header.addMetaDataLine(new VCFInfoHeaderLine(PON_COUNT, 1, VCFHeaderLineType.Integer, "how many samples had the variant"));
    header.addMetaDataLine(new VCFInfoHeaderLine(PON_TOTAL, 1, VCFHeaderLineType.Integer, "total depth"));
    header.addMetaDataLine(new VCFInfoHeaderLine(PON_MAX, 1, VCFHeaderLineType.Integer, "max depth"));
    header.addMetaDataLine(new VCFHeaderLine("PonInputSampleCount", String.valueOf(sampleSize)));
    writer.writeHeader(header);
}
 

private static void writeHotspots(@NotNull String hotspotVcf, @NotNull Map<ViccEntry, ViccExtractionResult> resultsPerEntry) {
    VariantContextWriter writer = new VariantContextWriterBuilder().setOutputFile(hotspotVcf)
            .setOutputFileType(VariantContextWriterBuilder.OutputType.VCF)
            .setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER)
            .modifyOption(Options.INDEX_ON_THE_FLY, false)
            .build();

    VCFHeader header = new VCFHeader(Sets.newHashSet(), Lists.newArrayList());
    writer.writeHeader(header);

    for (Map.Entry<VariantHotspot, HotspotAnnotation> entry : convertAndSort(resultsPerEntry).entrySet()) {
        VariantHotspot hotspot = entry.getKey();
        HotspotAnnotation annotation = entry.getValue();
        List<Allele> hotspotAlleles = buildAlleles(hotspot);

        VariantContext variantContext = new VariantContextBuilder().noGenotypes()
                .source("VICC")
                .chr(hotspot.chromosome())
                .start(hotspot.position())
                .alleles(hotspotAlleles)
                .computeEndFromAlleles(hotspotAlleles, (int) hotspot.position())
                .attribute("sources", annotation.sources())
                .attribute("feature",
                        ProteinKeyFormatter.toProteinKey(annotation.gene(), annotation.transcript(), annotation.proteinAnnotation()))
                .make();

        LOGGER.debug("Writing {}", variantContext);
        writer.add(variantContext);

    }
    writer.close();
}
 

private static void processVariants(@NotNull final String filePath, @NotNull final String outputVcf, @NotNull final String outputBed,
        boolean strelka) throws IOException {
    final VCFFileReader vcfReader = new VCFFileReader(new File(filePath), false);
    final VCFHeader outputHeader =
            strelka ? generateOutputHeader(vcfReader.getFileHeader(), StrelkaPostProcess.TUMOR_GENOTYPE) : vcfReader.getFileHeader();
    final BufferedWriter bedWriter = new BufferedWriter(new FileWriter(outputBed, false));
    final VariantContextWriter vcfWriter = new VariantContextWriterBuilder().setOutputFile(outputVcf)
            .setReferenceDictionary(outputHeader.getSequenceDictionary())
            .build();
    vcfWriter.writeHeader(outputHeader);

    Pair<PotentialMNVRegion, Optional<PotentialMNVRegion>> outputPair = ImmutablePair.of(PotentialMNVRegion.empty(), Optional.empty());
    for (final VariantContext rawVariant : vcfReader) {
        final VariantContext variant =
                strelka ? StrelkaPostProcess.simplifyVariant(rawVariant, StrelkaPostProcess.TUMOR_GENOTYPE) : rawVariant;

        final PotentialMNVRegion potentialMNVregion = outputPair.getLeft();
        outputPair = MNVDetector.addMnvToRegion(potentialMNVregion, variant);
        outputPair.getRight()
                .ifPresent(mnvRegion -> filterMnvRegion(mnvRegion).ifPresent(filteredRegion -> writeMnvRegionToFiles(filteredRegion,
                        vcfWriter,
                        bedWriter,
                        "\n")));
    }
    filterMnvRegion(outputPair.getLeft()).ifPresent(mnvRegion -> writeMnvRegionToFiles(mnvRegion, vcfWriter, bedWriter, ""));
    vcfWriter.close();
    vcfReader.close();
    bedWriter.close();
    LOGGER.info("Written output variants to {}. Written bed regions to {}.", outputVcf, outputBed);
}
 

private static void processVariants(@NotNull final String filePath, @NotNull final Slicer highConfidenceSlicer,
        @NotNull final String outputVcf, @NotNull final String sampleName, @NotNull final String tumorBam) {
    final VCFFileReader vcfReader = new VCFFileReader(new File(filePath), false);
    final VCFHeader outputHeader = generateOutputHeader(vcfReader.getFileHeader(), sampleName);
    final VariantContextWriter writer = new VariantContextWriterBuilder().setOutputFile(outputVcf)
            .setReferenceDictionary(outputHeader.getSequenceDictionary())
            .build();
    writer.writeHeader(outputHeader);
    final MNVValidator validator = ImmutableMNVValidator.of(tumorBam);
    final MNVMerger merger = ImmutableMNVMerger.of(outputHeader);

    Pair<PotentialMNVRegion, Optional<PotentialMNVRegion>> outputPair = ImmutablePair.of(PotentialMNVRegion.empty(), Optional.empty());

    final VariantContextFilter filter = new StrelkaPostProcess(highConfidenceSlicer);
    for (final VariantContext variantContext : vcfReader) {
        if (filter.test(variantContext)) {
            final VariantContext simplifiedVariant = StrelkaPostProcess.simplifyVariant(variantContext, sampleName);
            final PotentialMNVRegion potentialMNV = outputPair.getLeft();
            outputPair = MNVDetector.addMnvToRegion(potentialMNV, simplifiedVariant);
            outputPair.getRight().ifPresent(mnvRegion -> validator.mergeVariants(mnvRegion, merger).forEach(writer::add));
        }
    }
    validator.mergeVariants(outputPair.getLeft(), merger).forEach(writer::add);
    writer.close();
    vcfReader.close();
    LOGGER.info("Written output variants to " + outputVcf);
}
 

@Override
protected int doWork() {
    final ProgressLogger progress = new ProgressLogger(log, 10000);
    final List<String> sampleList = new ArrayList<String>();
    INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS);
    final Collection<CloseableIterator<VariantContext>> iteratorCollection = new ArrayList<CloseableIterator<VariantContext>>(INPUT.size());
    final Collection<VCFHeader> headers = new HashSet<VCFHeader>(INPUT.size());
    VariantContextComparator variantContextComparator = null;
    SAMSequenceDictionary sequenceDictionary = null;

    if (SEQUENCE_DICTIONARY != null) {
        sequenceDictionary = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(SEQUENCE_DICTIONARY).getFileHeader().getSequenceDictionary();
    }

    for (final File file : INPUT) {
        IOUtil.assertFileIsReadable(file);
        final VCFFileReader fileReader = new VCFFileReader(file, false);
        final VCFHeader fileHeader = fileReader.getFileHeader();
        if (fileHeader.getContigLines().isEmpty()) {
            if (sequenceDictionary == null) {
                throw new IllegalArgumentException(SEQ_DICT_REQUIRED);
            } else {
                fileHeader.setSequenceDictionary(sequenceDictionary);
            }
        }

        if (variantContextComparator == null) {
            variantContextComparator = fileHeader.getVCFRecordComparator();
        } else {
            if (!variantContextComparator.isCompatible(fileHeader.getContigLines())) {
                throw new IllegalArgumentException(
                        "The contig entries in input file " + file.getAbsolutePath() + " are not compatible with the others.");
            }
        }

        if (sequenceDictionary == null) sequenceDictionary = fileHeader.getSequenceDictionary();

        if (sampleList.isEmpty()) {
            sampleList.addAll(fileHeader.getSampleNamesInOrder());
        } else {
            if (!sampleList.equals(fileHeader.getSampleNamesInOrder())) {
                throw new IllegalArgumentException("Input file " + file.getAbsolutePath() + " has sample entries that don't match the other files.");
            }
        }
        
        // add comments in the first header
        if (headers.isEmpty()) {
            COMMENT.stream().forEach(C -> fileHeader.addMetaDataLine(new VCFHeaderLine("MergeVcfs.comment", C)));
        }

        headers.add(fileHeader);
        iteratorCollection.add(fileReader.iterator());
    }

    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException(String.format("Index creation failed. %s", SEQ_DICT_REQUIRED));
    }

    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setOutputFile(OUTPUT)
            .setReferenceDictionary(sequenceDictionary);

    if (CREATE_INDEX) {
        builder.setOption(Options.INDEX_ON_THE_FLY);
    } else {
        builder.unsetOption(Options.INDEX_ON_THE_FLY);
    }
    final VariantContextWriter writer = builder.build();

    writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false), sampleList));

    final MergingIterator<VariantContext> mergingIterator = new MergingIterator<VariantContext>(variantContextComparator, iteratorCollection);
    while (mergingIterator.hasNext()) {
        final VariantContext context = mergingIterator.next();
        writer.add(context);
        progress.record(context.getContig(), context.getStart());
    }

    CloserUtil.close(mergingIterator);
    writer.close();
    return 0;
}
 

@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    final ProgressLogger progress = new ProgressLogger(log, 10000);

    final VCFFileReader fileReader = new VCFFileReader(INPUT, false);
    final VCFHeader fileHeader = fileReader.getFileHeader();

    final SAMSequenceDictionary sequenceDictionary =
            SEQUENCE_DICTIONARY != null
                    ? SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(SEQUENCE_DICTIONARY).getSequenceDictionary()
                    : fileHeader.getSequenceDictionary();
    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
    }

    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setReferenceDictionary(sequenceDictionary)
            .clearOptions();
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);

    final VariantContextWriter snpWriter = builder.setOutputFile(SNP_OUTPUT).build();
    final VariantContextWriter indelWriter = builder.setOutputFile(INDEL_OUTPUT).build();
    snpWriter.writeHeader(fileHeader);
    indelWriter.writeHeader(fileHeader);

    int incorrectVariantCount = 0;

    final CloseableIterator<VariantContext> iterator = fileReader.iterator();
    while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
        if (context.isIndel()) indelWriter.add(context);
        else if (context.isSNP()) snpWriter.add(context);
        else {
            if (STRICT) throw new IllegalStateException("Found a record with type " + context.getType().name());
            else incorrectVariantCount++;
        }

        progress.record(context.getContig(), context.getStart());
    }

    if (incorrectVariantCount > 0) {
        log.debug("Found " + incorrectVariantCount + " records that didn't match SNP or INDEL");
    }

    CloserUtil.close(iterator);
    CloserUtil.close(fileReader);
    snpWriter.close();
    indelWriter.close();

    return 0;
}
 

@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    VCFFileReader in = null;
    VariantContextWriter out = null;
    try {// try/finally used to close 'in' and 'out'
        in = new VCFFileReader(INPUT, false);
        final List<VariantFilter> variantFilters = new ArrayList<>(4);
        variantFilters.add(new AlleleBalanceFilter(MIN_AB));
        variantFilters.add(new FisherStrandFilter(MAX_FS));
        variantFilters.add(new QdFilter(MIN_QD));
        if (JAVASCRIPT_FILE != null) {
            try {
                variantFilters.add(new VariantContextJavascriptFilter(JAVASCRIPT_FILE, in.getFileHeader()));
            } catch (final IOException error) {
                throw new PicardException("javascript-related error", error);
            }
        }
        final List<GenotypeFilter> genotypeFilters = CollectionUtil.makeList(new GenotypeQualityFilter(MIN_GQ), new DepthFilter(MIN_DP));
        final FilterApplyingVariantIterator iterator = new FilterApplyingVariantIterator(in.iterator(), variantFilters, genotypeFilters);

        final VCFHeader header = in.getFileHeader();
        // If the user is writing to a .bcf or .vcf, VariantContextBuilderWriter requires a Sequence Dictionary.  Make sure that the
        // Input VCF has one.
        final VariantContextWriterBuilder variantContextWriterBuilder = new VariantContextWriterBuilder();
        if (isVcfOrBcf(OUTPUT)) {
            final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();
            if (sequenceDictionary == null) {
                throw new PicardException("The input vcf must have a sequence dictionary in order to create indexed vcf or bcfs.");
            }
            variantContextWriterBuilder.setReferenceDictionary(sequenceDictionary);
        }
        out = variantContextWriterBuilder.setOutputFile(OUTPUT).build();
        header.addMetaDataLine(new VCFFilterHeaderLine("AllGtsFiltered", "Site filtered out because all genotypes are filtered out."));
        header.addMetaDataLine(new VCFFormatHeaderLine("FT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype filters."));
        for (final VariantFilter filter : variantFilters) {
            filter.headerLines().forEach(header::addMetaDataLine);
        }

        out.writeHeader(in.getFileHeader());

        while (iterator.hasNext()) {
            final VariantContext vc = iterator.next();
            progress.record(vc.getContig(), vc.getStart());
            out.add(vc);
        }
        return 0;
    } finally {
        CloserUtil.close(out);
        CloserUtil.close(in);
    }
}
 

@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    final VCFFileReader reader = new VCFFileReader(INPUT, false);
    final VCFHeader inputVcfHeader = new VCFHeader(reader.getFileHeader().getMetaDataInInputOrder());
    final SAMSequenceDictionary sequenceDictionary = inputVcfHeader.getSequenceDictionary();

    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
    }

    final ProgressLogger progress = new ProgressLogger(Log.getInstance(MakeSitesOnlyVcf.class), 10000);

    // Setup the site-only file writer
    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setOutputFile(OUTPUT)
            .setReferenceDictionary(sequenceDictionary);
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);
    else
        builder.unsetOption(Options.INDEX_ON_THE_FLY);
    final VariantContextWriter writer = builder.build();

    final VCFHeader header = new VCFHeader(inputVcfHeader.getMetaDataInInputOrder(), SAMPLE);
    writer.writeHeader(header);

    // Go through the input, strip the records and write them to the output
    final CloseableIterator<VariantContext> iterator = reader.iterator();
    while (iterator.hasNext()) {
        final VariantContext full = iterator.next();
        final VariantContext site = subsetToSamplesWithOriginalAnnotations(full, SAMPLE);
        writer.add(site);
        progress.record(site.getContig(), site.getStart());
    }

    CloserUtil.close(iterator);
    CloserUtil.close(reader);
    writer.close();

    return 0;
}