Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFHeader

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        IOUtil.assertFileIsWritable(OUTPUT);

        final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY);

        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()) {
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        return true;
    }

    /** Validates that all headers contain the same set of genotyped samples and that files are in order by position of first record. */
    private static void assertSameSamplesAndValidOrdering(final List<File> inputFiles) {
        final VCFHeader header = new VCFFileReader(inputFiles.get(0), false).getFileHeader();
        final SAMSequenceDictionary dict = header.getSequenceDictionary();
        final VariantContextComparator comparator = new VariantContextComparator(header.getSequenceDictionary());
        final List<String> samples = header.getGenotypeSamples();

        File lastFile = null;
        VariantContext lastContext = null;

        for (final File f : inputFiles) {
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        final VariantContextWriter out = VariantContextWriterFactory.create(outputFile, sequenceDictionary, options);

        final ProgressLogger progress = new ProgressLogger(log, 10000);
        VariantContext lastContext = null;
        File lastFile = null;
        VCFHeader firstHeader = null;
        VariantContextComparator comparator = null;

        for (final File f : inputFiles) {
            log.debug("Gathering from file: ", f.getAbsolutePath());
            final VCFFileReader variantReader = new VCFFileReader(f, false);
            final PeekableIterator<VariantContext> variantIterator = new PeekableIterator<VariantContext>(variantReader.iterator());
            final VCFHeader header = variantReader.getFileHeader();

            if (firstHeader == null) {
                firstHeader = header;
                out.writeHeader(firstHeader);
                comparator = new VariantContextComparator(firstHeader.getContigLines());
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    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()) {
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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

        final VCFFileReader in = new VCFFileReader(INPUT);
        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(VariantContextWriterFactory.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 = VariantContextWriterFactory.create(OUTPUT, outHeader.getSequenceDictionary(), options);
        out.writeHeader(outHeader);

        for (final VariantContext ctx : in) {
            out.add(ctx);
        }
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        final List<GenotypeFilter> genotypeFilters = CollectionUtil.makeList(new GenotypeQualityFilter(MIN_GQ), new DepthFilter(MIN_DP));
        final VCFFileReader in = new VCFFileReader(INPUT, false);
        final FilterApplyingVariantIterator iterator = new FilterApplyingVariantIterator(in.iterator(), variantFilters, genotypeFilters);

        final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).build();
        final VCFHeader header = in.getFileHeader();
        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) {
            for (final VCFFilterHeaderLine line : filter.headerLines()) {
                header.addMetaDataLine(line);
            }
        }

        out.writeHeader(in.getFileHeader());
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  protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    final ProgressLogger progress = new ProgressLogger(log, 10000);

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

    final SAMSequenceDictionary sequenceDictionary =
        SEQUENCE_DICTIONARY != null
            ? SAMFileReader.getSequenceDictionary(SEQUENCE_DICTIONARY)
            : 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()
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        // Gather up a file reader and file header for each input file. Check for sequence dictionary compatibility along the way.
        collectFileReadersAndHeaders(sampleList, samSequenceDictionary);

        // Create the merged output header from the input headers
        final VCFHeader outputHeader = new VCFHeader(VCFUtils.smartMergeHeaders(inputHeaders, false), sampleList);

        // Load entries into the sorting collection
        final SortingCollection<VariantContext> sortedOutput = sortInputs(inputReaders, outputHeader);

        // Output to the final file
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    }

    private void collectFileReadersAndHeaders(final List<String> sampleList, SAMSequenceDictionary samSequenceDictionary) {
        for (final File input : INPUT) {
            final VCFFileReader in = new VCFFileReader(input, false);
            final VCFHeader header = in.getFileHeader();
            final SAMSequenceDictionary dict = in.getFileHeader().getSequenceDictionary();
            if (dict == null || dict.isEmpty()) {
                if (null == samSequenceDictionary) {
                    throw new IllegalArgumentException("Sequence dictionary was missing or empty for the VCF: " + input.getAbsolutePath() + " Please add a sequence dictionary to this VCF or specify SEQUENCE_DICTIONARY.");
                }
                header.setSequenceDictionary(samSequenceDictionary);
            } else {
                if (null == samSequenceDictionary) {
                    samSequenceDictionary = dict;
                } else {
                    try {
                        samSequenceDictionary.assertSameDictionary(dict);
                    } catch (final AssertionError e) {
                        throw new IllegalArgumentException(e);
                    }
                }
            }
            if (sampleList.isEmpty()) {
                sampleList.addAll(header.getSampleNamesInOrder());
            } else {
                if ( !sampleList.equals(header.getSampleNamesInOrder())) {
                    throw new IllegalArgumentException("Input file " + input.getAbsolutePath() + " has sample names that don't match the other files.");
                }
            }
            inputReaders.add(in);
            inputHeaders.add(header);
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    if (SEQUENCE_DICTIONARY != null) sequenceDictionary = SAMFileReader.getSequenceDictionary(SEQUENCE_DICTIONARY);

    for (final File file : INPUT) {
      IOUtil.assertFileIsReadable(file);
      final VCFFileReader fileReader = new VCFFileReader(file, false);
      final VCFHeader fileHeader = fileReader.getFileHeader();

      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.");
        }
      }

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

    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()
                .setOutputFile(OUTPUT)
                .setReferenceDictionary(sequenceDictionary)
                .clearOptions();
        if (CREATE_INDEX)
            builder.setOption(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);
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