import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
@Override
public void initialize(final AnnotatorCompatible walker, final GenomeLocParser parser, final Set<VCFHeaderLine> headerLines) {
    boolean hasSBBSannotation = false;
    for (final VCFHeaderLine line : headerLines) {
        if (line instanceof VCFFormatHeaderLine) {
            final VCFFormatHeaderLine formatline = (VCFFormatHeaderLine) line;
            if (formatline.getID().equals(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME)) {
                hasSBBSannotation = true;
                break;
            }
        }
    }

    if (hasSBBSannotation) {
        logger.info("StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample " +
                "values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.");
        return;
    }

}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
/**
 * Add header entries.
 * 
 * @param header The {@link VCFHeader} to extend.
 */
public void addHeaders(VCFHeader header) {
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_DE_NOVO_PARENT_AD2,
			"Supporting read count for alternative allele in tentative de novo call > "
					+ options.getDeNovoMaxParentAd2()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_DE_NOVO_IN_SIBLING,
			"Non-ref genotype also seen in sibling"));

	header.addMetaDataLine(
			new VCFFormatHeaderLine(FORMAT_GT_DE_NOVO, 1, VCFHeaderLineType.Character,
					"Whether the variant looks de novo by genotype, one of {'Y', 'N'}."));
	header.addMetaDataLine(
			new VCFFormatHeaderLine(FORMAT_PARENTS_REF, 1, VCFHeaderLineType.Character,
					"Whether both parent's genotype is reference, one of {'Y', 'N'}."));

	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_ONE_PARENT_FILTERED,
			"One parent was filtered or no-call, filter child as well, important for inheritance "
					+ "filtration as filtered variants count as no-call which counts as "
					+ "wild-card by default; \"one/both parents filtered\" don't count. (enabled: "
					+ options.isApplyParentGtFilteredFilters() + ")"));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_BOTH_PARENTS_FILTERED,
			"Both parents are filtered or no-call, filter child as well, important for inheritance "
					+ "filtration as filtered variants count as no-call which counts as "
					+ "wild-card by default; \"one/both parents filtered\" don't count. (enabled: "
					+ options.isApplyParentGtFilteredFilters() + ")"));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public static VCFFormatHeaderLine renameVCFFormatHeaderLine(VCFFormatHeaderLine h,String name)
{
if(h.getCountType()==VCFHeaderLineCount.INTEGER)
	{
	return new VCFFormatHeaderLine(
			name,
			h.getCount(),
			h.getType(),
			h.getDescription()
			);
	}
else
	{
	return new VCFFormatHeaderLine(
			name,
			h.getCountType(),
			h.getType(),
			h.getDescription()
			);
	}
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public static Set<VCFHeaderLine> getVCFHeaderInfo() {
    Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();


    headerInfo.add(new VCFFilterHeaderLine("REJECT", "Rejected as a confident somatic mutation"));
    headerInfo.add(new VCFFilterHeaderLine("PASS", "Accept as a confident somatic mutation"));

    // TODO: what fields do we need here
    VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true,
            VCFConstants.MAPPING_QUALITY_ZERO_KEY,
            VCFConstants.DBSNP_KEY,
            VCFConstants.SOMATIC_KEY);

    // TODO copy from TCGA spec..
    headerInfo.add(new VCFInfoHeaderLine("VT", 1, VCFHeaderLineType.String, "Variant type, can be SNP, INS or DEL"));


    VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true,
            VCFConstants.GENOTYPE_KEY,
            VCFConstants.GENOTYPE_QUALITY_KEY,
            VCFConstants.DEPTH_KEY,
            VCFConstants.GENOTYPE_ALLELE_DEPTHS,
            VCFConstants.GENOTYPE_PL_KEY);

    // cancer-specific
    // TODO: push to VCFConstants in GATK
    headerInfo.add(new VCFFormatHeaderLine("FA", VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele fraction of the alternate allele with regard to reference"));
    headerInfo.add(new VCFFormatHeaderLine("SS", 1, VCFHeaderLineType.Integer, "Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown"));
    headerInfo.add(new VCFFormatHeaderLine(VCFConstants.RMS_BASE_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Average base quality for reads supporting alleles"));

    return headerInfo;
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
@NotNull
static VCFHeader generateOutputHeader(@NotNull final VCFHeader header, @NotNull final String sampleName) {
    final VCFHeader outputVCFHeader = new VCFHeader(header.getMetaDataInInputOrder(), Sets.newHashSet(sampleName));
    outputVCFHeader.addMetaDataLine(
            new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.R, VCFHeaderLineType.Integer,
                    "Allelic depths for the ref and alt alleles in the order listed"));
    outputVCFHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
    outputVCFHeader.addMetaDataLine(
            new VCFHeaderLine("StrelkaGATKCompatibility", "Added GT fields to strelka calls for gatk compatibility."));
    return outputVCFHeader;
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
/**
 * Add header entries.
 * 
 * @param header The {@link VCFHeader} to extend.
 */
public void addHeaders(VCFHeader header) {
	if (!header.hasFormatLine("FT")) header.addMetaDataLine(new VCFFormatHeaderLine("FT", 1,
			VCFHeaderLineType.String, "Filters applied to genotype call"));

	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MAX_COV,
			"Genotype has coverage >" + options.getMaxCov()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MIN_COV_HET,
			"Het. genotype call has coverage <" + options.getMinGtCovHet()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MIN_COV_HOM_ALT,
			"Hom. alt genotype call has coverage <" + options.getMinGtCovHomAlt()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MIN_GQ,
			"Genotype has quality (GQ) <" + options.getMinGtGq()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MIN_AAF_HET,
			"Het. genotype has alternative allele fraction <" + options.getMinGtAafHet()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MAX_AAF_HET,
			"Het. genotype has alternative allele fraction >" + options.getMaxGtAafHet()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MIN_AAF_HOM_ALT,
			"Hom. alt genotype has alternative allele fraction <"
					+ options.getMinGtAafHomAlt()));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_GT_MAX_AAF_HOM_REF,
			"Wild-type genotype has AAF >" + options.getMaxGtAafHomRef()));

	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_VAR_ALL_AFFECTED_GTS_FILTERED,
			"The genotype calls of all affected individuals have been filtered for this variant."));

	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_VAR_MAX_FREQUENCY_AD,
			"Variant frequency >" + options.getMaxAlleleFrequencyAd()
					+ " (threshold for AD inheritance), variant will be annotated with "
					+ "compatibility with dominant inheritance regardlessly"));
	header.addMetaDataLine(new VCFFilterHeaderLine(FILTER_VAR_MAX_FREQUENCY_AR,
			"Variant frequency >" + options.getMaxAlleleFrequencyAd()
					+ " (threshold for AR inheritance), variant will not be considered for "
					+ "composite recessive inheritance but for homozygous recessive inheritance "
					+ "regardlessly"));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
/** build a table describing the FORMAT column */
private Tab buildFormatHeaderTab(final VCFHeader header)
	{
       final TableView<VCFFormatHeaderLine> table=new TableView<>(FXCollections.observableArrayList(header.getFormatHeaderLines()));
       table.getColumns().add(makeColumn("ID", F->F.getID()));
       table.getColumns().add(makeColumn("Type", F->F.getType()==null?null:F.getType().name()));
       table.getColumns().add(makeColumn("Count", F->F.isFixedCount()?F.getCount():null));
       table.getColumns().add(makeColumn("Description", F->F.getDescription()));
       final Tab tab=new Tab("FORMAT",table);
       tab.setClosable(false);
       table.setPlaceholder(new Label("No FORMAT defined."));
       return tab;
	}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
@Override
public void writeHeader(final VCFHeader header) {
	final VCFHeader header2= new VCFHeader(header);
	
	final String termlist = String.join(", ",CtxWriterFactory.this.user_terms.stream().
				map(S->S.getAcn()+"("+S.getLabel()+")").
				collect(Collectors.toSet()))
				;
	if(!CtxWriterFactory.this.filterIn.isEmpty()) {
		header2.addMetaDataLine(new VCFFilterHeaderLine(CtxWriterFactory.this.filterIn,
				"Variant having SO terms:"+ termlist));
		}
	if(!CtxWriterFactory.this.filterOut.isEmpty()) {
		header2.addMetaDataLine(new VCFFilterHeaderLine(CtxWriterFactory.this.filterOut,
				"Variant non having SO terms :" + termlist));
		}
	
	if(!StringUtil.isBlank(this.filterGenotypesStr) &&
		!GT_FILTER_RESET_TO_NOCALL.equals(this.filterGenotypesStr))
		{
		header2.addMetaDataLine(new VCFFormatHeaderLine(
				VCFConstants.GENOTYPE_FILTER_KEY,
				1,VCFHeaderLineType.String,
				"Genotype was filterered by vcffilterso : "+this.filterGenotypesStr
				));
		}
	
	AbstractPredictionHandler ph = new VepPredictionHandler(header);
	if(ph.isValid()) this.predictionHandlers.add(ph);
	ph = new SnpEffPredictionHandler(header);
	if(ph.isValid()) this.predictionHandlers.add(ph);
	ph = new MyPredictionHandler(header);
	if(ph.isValid()) this.predictionHandlers.add(ph);
	ph = new AnnPredictionHandler(header);
	if(ph.isValid()) this.predictionHandlers.add(ph);
	
	super.writeHeader(header2);
	}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public IgvReview()
{
this.preferences = Preferences.userNodeForPackage(IgvReview.class);

final String userName=System.getProperty("user.name", "user").replace(" ", "_");
this.reviewFormat = new VCFFormatHeaderLine(userName+"_REVIEW",1,VCFHeaderLineType.String,"Review genotypes by "+userName);
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public List<VCFFormatHeaderLine> getDescriptions() {
    return Arrays.asList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
@Override
public List<VCFFormatHeaderLine> getDescriptions() { return Collections.singletonList(new VCFFormatHeaderLine(getKeyNames().get(0), 4, VCFHeaderLineType.Integer, "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.")); }
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public List<VCFFormatHeaderLine> getDescriptions() {
    return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(
new VCFFormatHeaderLine(getKeyNames().get(0), 1,
        VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); }
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public List<VCFFormatHeaderLine> getDescriptions() {
    return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype"));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public static VCFFormatHeaderLine getFormatLine(final String id) {
	return formatLines.get(id);
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
public static Set<VCFFormatHeaderLine> getAllFormatLines() {
	return Collections.unmodifiableSet(new HashSet<>(formatLines.values()));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
private static void addFormatLine(final VCFFormatHeaderLine line) {
	Utils.nonNull(line);
	formatLines.put(line.getID(), line);
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
@Override
public List<VCFFormatHeaderLine> getDescriptions() {
	return Arrays.asList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
private static void addFormatLine(final VCFFormatHeaderLine line) {
	formatLines.put(line.getID(), line);
}
 

import htsjdk.variant.vcf.VCFFormatHeaderLine; //导入依赖的package包/类
private VCFHeader generateHeader(String name, String chromosome) {

		Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
		Set<String> additionalColumns = new HashSet<String>();

		headerLines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_0.getFormatString(),
				VCFHeaderVersion.VCF4_0.getVersionString()));

		headerLines.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));

		additionalColumns.add(name);

		SAMSequenceDictionary sequenceDict = generateSequenceDictionary(chromosome);

		VCFHeader header = new VCFHeader(headerLines, additionalColumns);
		header.setSequenceDictionary(sequenceDict);

		return header;

	}