Package htsjdk.variant.variantcontext.writer

Examples of htsjdk.variant.variantcontext.writer.VariantContextWriter.writeHeader()

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        FeatureCodec codec = CodecFactory.getCodec(inpath, genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(inpath, codec, false);
        VCFHeader header0 = (VCFHeader) bfs.getHeader();

        VariantContextWriter writer = getWriter();
        writer.writeHeader(header0);
        writer.close();

        AbstractFeatureReader<Feature, ?> bfs1 = AbstractFeatureReader.getFeatureReader(outFile.getAbsolutePath(), codec, false);
        VCFHeader header1 = (VCFHeader) bfs1.getHeader();
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        Iterable<VCFVariant> iter0 = bfs.iterator();
        List<VCFVariant> list0 = new ArrayList<VCFVariant>();
        VCFHeader header0 = (VCFHeader) bfs.getHeader();

        VariantContextWriter writer = getWriter();
        writer.writeHeader(header0);
        for (VCFVariant var : iter0) {
            writer.add(var.getVariantContext());
            list0.add(var);
        }
        writer.close();
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        EnumSet<Options> options = VariantContextWriterFactory.DEFAULT_OPTIONS;
        options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
        options.remove(Options.INDEX_ON_THE_FLY);
        VariantContextWriter writer = VariantContextWriterFactory.create(outputStream, seqDict, options);

        writer.writeHeader(this.header);

        while(features.hasNext()){
            writer.add(features.next().getVariantContext());
        }
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                System.out.print(count);
            else
                System.out.print(".");
            if (firstFile){
                VCFHeader header = (VCFHeader)reader.getHeader();
                outputWriter.writeHeader(header);
                firstFile = false;
            }

            Iterator<VariantContext> it = reader.iterator();
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            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());
            }

            if (lastContext != null && variantIterator.hasNext()) {
                final VariantContext vc = variantIterator.peek();
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        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();
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        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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            for (final VCFFilterHeaderLine line : filter.headerLines()) {
                header.addMetaDataLine(line);
            }
        }

        out.writeHeader(in.getFileHeader());

        while (iterator.hasNext()) {
            out.add(iterator.next());
        }
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            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()) {
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        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.getChr(), variantContext.getStart());
        }
        out.close();
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