Java VariantContextWriterBuilder类代码示例

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的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; //导入依赖的package包/类
private static void processVariants(@NotNull final String filePath, @NotNull final Slicer highConfidenceSlicer,
        @NotNull final String outputVcf, @NotNull final String sampleName, @NotNull final String tumorBam) throws HartwigException {
    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);
    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.fitsMNVRegion(potentialMNV, simplifiedVariant);
            outputPair.getRight().ifPresent(mnvRegion -> validator.mergeVariants(mnvRegion).forEach(writer::add));
        }
    }
    validator.mergeVariants(outputPair.getLeft()).forEach(writer::add);
    writer.close();
    vcfReader.close();
    LOGGER.info("Written output variants to " + outputVcf);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的package包/类
private static void processVariants(@NotNull final String filePath, @NotNull final String outputVcf, @NotNull final String tumorBam) {
    final VCFFileReader vcfReader = new VCFFileReader(new File(filePath), false);
    final VariantContextWriter vcfWriter = new VariantContextWriterBuilder().setOutputFile(outputVcf)
            .setReferenceDictionary(vcfReader.getFileHeader().getSequenceDictionary())
            .build();
    vcfWriter.writeHeader(vcfReader.getFileHeader());
    final MNVValidator validator = ImmutableMNVValidator.of(tumorBam);
    Pair<PotentialMNVRegion, Optional<PotentialMNVRegion>> outputPair = ImmutablePair.of(PotentialMNVRegion.empty(), Optional.empty());
    for (final VariantContext variant : vcfReader) {
        final PotentialMNVRegion potentialMNV = outputPair.getLeft();
        outputPair = MNVDetector.fitsMNVRegion(potentialMNV, variant);
        outputPair.getRight().ifPresent(mnvRegion -> validator.mergeVariants(mnvRegion).forEach(vcfWriter::add));
    }
    validator.mergeVariants(outputPair.getLeft()).forEach(vcfWriter::add);
    vcfWriter.close();
    vcfReader.close();
    LOGGER.info("Written output variants to " + outputVcf);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的package包/类
/**
 * 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));
  }
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的package包/类
public static List<String> vcfHeaderToStrings(VCFHeader header) {

	    File fakeVCFFile;
	    List<String> str= new ArrayList<String>();
	    try {
	    	fakeVCFFile = Utils.createTempFile(".vcfheader", ".vcf");
		    fakeVCFFile.deleteOnExit();
			final VariantContextWriter writer = new VariantContextWriterBuilder()
		            .setOutputFile(fakeVCFFile)
		            .setReferenceDictionary(header.getSequenceDictionary())
		            .setOptions(EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Options.WRITE_FULL_FORMAT_FIELD))
		            .build();
		    writer.writeHeader(header);
		    writer.close();
		    BufferedReader br= new BufferedReader(new FileReader(fakeVCFFile));
		    String line= br.readLine();
		    while(line != null){
		    	str.add(line);
		    	line= br.readLine();
		    }
		    br.close();
		} catch (IOException e) {
			e.printStackTrace();
		}
		return str;
	}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的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; //导入依赖的package包/类
/**
 * 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) throws IOException {
    final String extension;

    if (vcfFile.getAbsolutePath().endsWith(".vcf")) extension = ".vcf";
    else if (vcfFile.getAbsolutePath().endsWith(".vcf.gz")) extension = ".vcf.gz";
    else
        throw new IllegalArgumentException("couldn't find a .vcf or .vcf.gz ending for input file " + vcfFile.getAbsolutePath());

    File output = createTemporaryIndexedVcfFile(tempFilePrefix, extension);

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

    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);
    }
    out.close();
    in.close();
    return output;
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的package包/类
private void init(
		OutputStream output, VCFHeader header, final boolean writeHeader)
	throws IOException
{
	final BCFStoppableOutputStream stopOut =
		new BCFStoppableOutputStream(!writeHeader, output);

	writer = new VariantContextWriterBuilder().clearOptions()
			.setOption(Options.FORCE_BCF)
			.setOutputBCFStream(stopOut).build();

	writer.writeHeader(header);
	stopOut.stopped = false;

	setInputHeader(header);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的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; //导入依赖的package包/类
private void initBuilder(OutputStream os, boolean doNotWriteGenotypes, 
		boolean allowMissingFieldsInHeader) {
	builder = new VariantContextWriterBuilder();
	builder.clearOptions();
	if(doNotWriteGenotypes) {
		builder.setOption(Options.DO_NOT_WRITE_GENOTYPES);
	}
	if(allowMissingFieldsInHeader) {
		builder.setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
	}
	builder.setOutputStream(os);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的package包/类
private static void processVariants(@NotNull final String filePath, @NotNull final String outputVcf, @NotNull final String outputBed,
        boolean strelka) throws IOException, HartwigException {
    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.fitsMNVRegion(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);
}
 

import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; //导入依赖的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;
}