Java VariantContextWriterBuilder.build方法代码示例

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
public static VariantContextWriter createVCFWriter(final File outFile,VCFHeader header) {
	Utils.nonNull(outFile);
	VariantContextWriterBuilder vcWriterBuilder = new VariantContextWriterBuilder().clearOptions()
			.setOutputFile(outFile);

	if (lenientVCFProcessing) {
		vcWriterBuilder = vcWriterBuilder.setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
	}

	if (createOutputVariantIndex && null != header) {
		vcWriterBuilder = vcWriterBuilder.setOption(Options.INDEX_ON_THE_FLY);
	}

	if (createOutputVariantMD5) {
		vcWriterBuilder.setCreateMD5();
	}

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

	return vcWriterBuilder.build();
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
/** 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();
    }
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
private static VariantContextWriter getVariantContextWriter(final OutputStream outputStream,
                                                            final SAMSequenceDictionary referenceSequenceDictionary) {
    VariantContextWriterBuilder vcWriterBuilder = new VariantContextWriterBuilder()
            .clearOptions()
            .setOutputStream(outputStream);

    if (null != referenceSequenceDictionary) {
        vcWriterBuilder = vcWriterBuilder.setReferenceDictionary(referenceSequenceDictionary);
    }
    // todo: remove this when things are solid?
    vcWriterBuilder = vcWriterBuilder.setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
    for (final Options opt : new Options[]{}) {
        vcWriterBuilder = vcWriterBuilder.setOption(opt);
    }

    return vcWriterBuilder.build();
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
/**
 * Return a new {@link VariantContextWriter} that uses the header from <code>reader</code> but has the header
 * extended header through {@link #extendHeaderFields}.
 *
 * @param header
 *            the VCF header to use for the construction
 * @param fileName
 *            path to output file
 * @param additionalHeaderLines
 *            additional {@link VCFHeaderLine}s to add
 * @param generateIndex
 *            whether or not to generate an index
 * @return A correct writer for variantContexts
 */
public static VariantContextWriter openVariantContextWriter(VCFHeader header, String fileName,
		Collection<VCFHeaderLine> additionalHeaderLines, boolean generateIndex) {
	VariantContextWriterBuilder builder = makeBuilder(header);
	builder.setOutputFile(new File(fileName));
	if (!generateIndex)
		builder.unsetOption(Options.INDEX_ON_THE_FLY);

	// construct VariantContextWriter and write out header
	VariantContextWriter out = builder.build();
	final VCFHeader updatedHeader = extendHeaderFields(new VCFHeader(header));
	for (VCFHeaderLine headerLine : additionalHeaderLines)
		updatedHeader.addMetaDataLine(headerLine);
	out.writeHeader(updatedHeader);
	return out;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
/**
 * create a VariantContextWriter
 * @param OUT output file or null to stdout
 * @return
 * @throws IOException
 */
public static  VariantContextWriter createVariantContextWriter(final File OUT) throws IOException
	{
	if(OUT==null)
		{
		return createVariantContextWriterToStdout();
		}
	else
		{
		IOUtil.assertFileIsWritable(OUT);
		final VariantContextWriterBuilder vcwb=new VariantContextWriterBuilder();
		vcwb.setCreateMD5(false);
		vcwb.setReferenceDictionary(null);
		vcwb.clearOptions();
		vcwb.setOutputFile(OUT);
		return new VariantContextWriterDelayedFlush(vcwb.build());
		}
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
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;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
@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;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
/**
 * 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 outFile output File 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 File outFile,
        final SAMSequenceDictionary referenceDictionary,
        final boolean createMD5,
        final Options... options)
{
    Utils.nonNull(outFile);

    VariantContextWriterBuilder vcWriterBuilder =
            new VariantContextWriterBuilder().clearOptions().setOutputFile(outFile);

    if (VariantContextWriterBuilder.OutputType.UNSPECIFIED == getVariantFileTypeFromExtension(outFile)) {
        // 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(outFile.getPath())));
        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();
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
private VariantContextWriter openOutputFile() {
	VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
			.setReferenceDictionary(fasta.getSequenceDictionary()).setOutputFile(options.getPathOutputVCF());
	if (options.getPathOutputVCF().endsWith(".gz") || options.getPathOutputVCF().endsWith(".bcf"))
		builder.setOption(Options.INDEX_ON_THE_FLY);
	else
		builder.unsetOption(Options.INDEX_ON_THE_FLY);
	VariantContextWriter writer = builder.build();

	VCFHeader header = new VCFHeader();
	int i = 0;
	for (SAMSequenceRecord record : fasta.getSequenceDictionary().getSequences()) {
		Map<String, String> mapping = new TreeMap<String, String>();
		mapping.put("ID", record.getSequenceName());
		mapping.put("length", Integer.toString(record.getSequenceLength()));
		header.addMetaDataLine(new VCFContigHeaderLine(mapping, i++));
	}

	header.addMetaDataLine(new VCFSimpleHeaderLine("ALT", "ERROR", "Error in conversion"));
	header.addMetaDataLine(new VCFFilterHeaderLine("PARSE_ERROR",
			"Problem in parsing original HGVS variant string, written out as variant at 1:g.1N>N"));
	header.addMetaDataLine(new VCFInfoHeaderLine("ERROR_MESSAGE", 1, VCFHeaderLineType.String, "Error message"));
	header.addMetaDataLine(new VCFInfoHeaderLine("ORIG_VAR", 1, VCFHeaderLineType.String,
			"Original HGVS variant string from input file to hgvs-to-vcf"));

	writer.writeHeader(header);

	return writer;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
@Override
public void open(final ExecutionContext executionContext) throws ItemStreamException {
	if(this.filenameFactory==null) throw new ItemStreamException("resource is not defined");
	try {
		final String filename = this.filenameFactory.apply(executionContext);
		if(StringUtil.isBlank(filename)) throw new ItemStreamException("No output file defined.");
		if(LOG.isInfoEnabled()) LOG.info("Opening "+filename+" for writing");
		
		if(!Arrays.stream(IOUtil.VCF_EXTENSIONS).anyMatch(SUFF->filename.endsWith(SUFF)))
			{
			throw new ItemStreamException("Bad extension for a VCF file:" + filename);
			}
		final File vcfFile = new File(filename);
		VCFHeader header= SpringBatchUtils.getVcfHeader(executionContext);
		final VariantContextWriterBuilder vcwb = new VariantContextWriterBuilder();
		vcwb.setOutputFile(vcfFile);
		if(this.reference!=null)
			{
			final SAMSequenceDictionary dic=SAMSequenceDictionaryExtractor.extractDictionary(this.reference);
			vcwb.setReferenceDictionary(dic);
			if(header.getSequenceDictionary()==null) {
				header = new VCFHeader(header);
				header.setSequenceDictionary(dic);
				}
			}
		else
			{
			vcwb.setReferenceDictionary(header.getSequenceDictionary());
			}
		vcwb.setCreateMD5(this.createMD5);
		this.vcw = vcwb.build();
		this.vcw.writeHeader(header);
		}
	catch(final Exception err)
		{
		priv_close();
		throw new ItemStreamException(err);
		}
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
public static  VariantContextWriter createVariantContextWriterToOutputStream(final OutputStream ostream)
{
final VariantContextWriterBuilder vcwb=new VariantContextWriterBuilder();
vcwb.setCreateMD5(false);
vcwb.setOutputStream(ostream);
vcwb.setReferenceDictionary(null);
vcwb.clearOptions();
return new VariantContextWriterDelayedFlush(vcwb.build());
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
@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;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
@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 (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);

    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;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
@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);

    try {
        builder.setOutputStream(new FileOutputStream(OUTPUT));
    } catch (final FileNotFoundException ex ) {
        throw new PicardException("Could not open " + OUTPUT.getAbsolutePath() + ": " + ex.getMessage(), ex);
    }

    final VariantContextWriter vcfWriter = builder.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;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入方法依赖的package包/类
private int doVcfToVcf(String inputName, final VcfIterator vcfIn,final File outFile) throws IOException {


SortingVCFWriter sortingVCW=null;
VariantContextWriterBuilder vcwb=new VariantContextWriterBuilder();
VariantContextWriter w=null;
try {
	SAMSequenceDictionary dict = vcfIn.getHeader().getSequenceDictionary();
	if(dict!=null) vcwb.setReferenceDictionary(dict);
	
	vcwb.setOutputFile(outFile);
	vcwb.setOutputFileType(OutputType.BLOCK_COMPRESSED_VCF);
	w = vcwb.build();
	
	if(this.sort)
		{
		LOG.info("Creating a sorting writer");
		sortingVCW= new SortingVCFWriter(w);
		w=sortingVCW;
		}
	
	w.writeHeader(vcfIn.getHeader());
	SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(vcfIn.getHeader());
	while(vcfIn.hasNext())
		{
		w.add(progress.watch(vcfIn.next()));
		}
	progress.finish();
	
	w.close();
	w=null;
	return RETURN_OK;
	} 
catch (Exception e)
	{
	if(outFile.exists() && outFile.isFile())
		{
		LOG.warn("Deleting "+outFile);
		outFile.delete();
		File tbi = new File(outFile.getPath()+TabixUtils.STANDARD_INDEX_EXTENSION);
		if(tbi.exists() && tbi.isFile()) tbi.delete();
		}
	LOG.error(e);
	return -1;
	}
finally
	{
	CloserUtil.close(w);
	}
}