Package htsjdk.variant.variantcontext.writer

Examples of htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build()

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                .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
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                .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()) {
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                .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();
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