Java VCFHeaderLineType.String方法代码示例

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
public static VCFHeaderLineType checkType(String type) {
	type = type.trim().toLowerCase();
	if(type.equals("integer")) {
		return VCFHeaderLineType.Integer;
	} else if(type.equals("float")) {
		return VCFHeaderLineType.Float;
	} else if(type.equals("string")) {
		return VCFHeaderLineType.String;
	} else if(type.equals("character")) {
		return VCFHeaderLineType.Character;
	} else if(type.equals("flag")) {
		return VCFHeaderLineType.Flag;
	} else {
		throw new IllegalArgumentException(ErrorMsg.VU_LINE_TYPE_ERR);
	}
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
@SuppressWarnings("unchecked")
@Override
public boolean filterLine(final T obj, String line) {
	
	if(line.startsWith(BEGIN)) {
		if(currentField != null) {
			Map<String, VCFInfoHeaderLine> infoMap = (Map<String, VCFInfoHeaderLine>)obj;
			infoMap.put(currentField, new VCFInfoHeaderLine(currentField, count, type, desc));
		}
		currentField = line.substring(1);
		if(currentField.trim().equals("")) throw new IllegalArgumentException("Field name is empty, please check filed name starts with @");
		desc = "";
		count = VCFHeaderLineCount.UNBOUNDED;
		type = VCFHeaderLineType.String;
		
		return false;
	} else if(line.equals("") || line.startsWith(COMMENT_LINE)) {
		return false;
	} else {
		return true;
	}
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
private void addHeaders(VCFHeader header, String prefix, String infix, String note) {
    VCFInfoHeaderLine infoClinVarBasicInfo = new VCFInfoHeaderLine(prefix + infix + "BASIC_INFO",
            VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String,
            "Annotation of basic info with the form 'allele | hgvs string | origin'" + note);
    header.addMetaDataLine(infoClinVarBasicInfo);

    VCFInfoHeaderLine infoClinVarVarInfo = new VCFInfoHeaderLine(prefix + infix + "VAR_INFO",
            VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String,
            "Annotation of variant source information of the form 'allele | db name | id in db | origins'" + note);
    header.addMetaDataLine(infoClinVarVarInfo);
    
    VCFInfoHeaderLine infoClinVarDiseaseInfo = new VCFInfoHeaderLine(prefix + infix + "DISEASE_INFO",
            VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String,
            "Annotation of disease information of the form 'allele | significance | disease db | id in disease db "
                    + "| name in disease db | revision status | clinical accession'" + note);
    header.addMetaDataLine(infoClinVarDiseaseInfo);
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
@Override
public void writeHeader(final VCFHeader header) {
	this.limitToThoseFilters = 
			CtxWriterFactory.this.onlyThoseFiltersTagStr.stream().flatMap(
					S->Arrays.asList(S.split("[, ]")).stream()).
					filter(S->!StringUtil.isBlank(S)).
					collect(Collectors.toSet())
					;
	this.infoHeaderLine = new VCFInfoHeaderLine(
			CtxWriterFactory.this.infoName.trim(),
			VCFHeaderLineCount.UNBOUNDED,
			VCFHeaderLineType.String,
			"Variant was previously FILTERed with the given values."
			);
	if(header.getInfoHeaderLine(infoHeaderLine.getID())!=null)
		{
		throw new JvarkitException.UserError("INFO["+this.infoHeaderLine.getID()+"] already exists in input VCF.");
		}
	
	
	final VCFHeader h2= new VCFHeader(header);	
	h2.addMetaDataLine(this.infoHeaderLine);
	super.writeHeader(h2);
	}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
public void setBedHeaderInfo(String dbLabel) {
		if(count == null) {
			System.err.println("You should set number for field " + name + " of bed file " + dbLabel + ", or we will use 'number=.' instead. ");
			count = VCFHeaderLineCount.UNBOUNDED;
		}
		if(type == null) {
			System.err.println("You should set type for field " + name + " of bed file " + dbLabel + ", or we will use 'type=string' instead. ");
			type = VCFHeaderLineType.String;
		}
//		if(count == null || type == null) throw new IllegalArgumentException("DB format is bed, please set number and type for field name " + name);
		this.vcfInfo = new VCFInfoHeaderLine((outName != null) ? outName:getName() , count, type, description);
	}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
public InfoItem(VCFInfoHeaderLine line) {
    this.name = line.getID();
    if (line.getCountType() != VCFHeaderLineCount.INTEGER) {
        this.type = VCFHeaderLineType.String;
    } else {
        this.type = line.getType();
    }
    this.description = line.getDescription();
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
public void extendHeader(VCFHeader vcfHeader, String prefix) {
	VCFInfoHeaderLine inheritanceLine = new VCFInfoHeaderLine(key(prefix), VCFHeaderLineCount.UNBOUNDED,
			VCFHeaderLineType.String, "Compatible inheritance modes (AD, AR, XD, XR, MT)");
	vcfHeader.addMetaDataLine(inheritanceLine);
	VCFInfoHeaderLine subInheritanceLine = new VCFInfoHeaderLine(keySub(prefix), VCFHeaderLineCount.UNBOUNDED,
			VCFHeaderLineType.String,
			"Extra annotation for recessive inheritance sub type (AR_HOM_ALT, AR_COMP_HET, XR_HOM_ALT, XR_COMP_HET)");
	vcfHeader.addMetaDataLine(subInheritanceLine);
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
/**
 * Extend a {@link VCFHeader} with the given <code>fields</code>.
 *
 * @param header
 *            the {@link VCFHeader} to extend
 * @return extended VCFHeader
 */
public static VCFHeader extendHeaderFields(VCFHeader header) {
	// add INFO line for standardized ANN field
	VCFInfoHeaderLine annLine = new VCFInfoHeaderLine("ANN", 1, VCFHeaderLineType.String,
			Annotation.VCF_ANN_DESCRIPTION_STRING);
	header.addMetaDataLine(annLine);
	return header;
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
@Override
public void writeHeader(final VCFHeader header) {
	final File srcbedfile = this.tabixFile==null?this.treeMapFile:this.tabixFile;
	this.vcfDict = header.getSequenceDictionary();
	final VCFHeader h2=new VCFHeader(header);
	this.infoHeader= 
			new VCFInfoHeaderLine(
					this.infoName,
					VCFHeaderLineCount.UNBOUNDED,
					VCFHeaderLineType.String,
					"metadata added from "+ srcbedfile+
					" . Format was "+this.formatPattern
					);
	
	this.filterOverlap = 
			(this.filterOverlapStr==null || this.filterNoOverlapStr.trim().isEmpty()?null:
			new VCFFilterHeaderLine(this.filterOverlapStr, "Variant overlap with "+srcbedfile)	
			);
	
	this.filterNoOverlap = 
			(this.filterNoOverlapStr==null || this.filterNoOverlapStr.trim().isEmpty()?null:
			new VCFFilterHeaderLine(this.filterNoOverlapStr, "Variant having NO overlap with "+srcbedfile)	
			);
	
	if(this.filterOverlap!=null) h2.addMetaDataLine(this.filterOverlap);
	if(this.filterNoOverlap!=null) h2.addMetaDataLine(this.filterNoOverlap);
	
	h2.addMetaDataLine(this.infoHeader);
	//addMetaData(h2);
	super.writeHeader(h2);
	}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的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.VCFHeaderLineType; //导入方法依赖的package包/类
/** create a parser without the VCF header */
public AnnPredictionParser createDefaultParser() 
	{
	final VCFHeader tmpheader=new VCFHeader();
	final VCFInfoHeaderLine info=new VCFInfoHeaderLine(
			AnnPredictionParser.getDefaultTag(),
			VCFHeaderLineCount.UNBOUNDED,
			VCFHeaderLineType.String,
			""
			);
	tmpheader.addMetaDataLine(info);
	return new AnnPredictionParser(tmpheader, getTag());
	}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
public void initSnpEffParser(final String definition)
{
failIf(definition==null || definition.trim().isEmpty(),"SnpEff definition is empty");
final VCFHeader header=new VCFHeader();
final VCFInfoHeaderLine info=new VCFInfoHeaderLine(
		VepPredictionParser.getDefaultTag(),
		VCFHeaderLineCount.UNBOUNDED,
		VCFHeaderLineType.String,
		definition
		);
header.addMetaDataLine(info);
this.vepPredictionParser=new VepPredictionParserFactory(header).get();
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
private static boolean parseOtherGenotypeFields(String field, VariantContext vc,
    ListValue.Builder lvBuilder, Genotype g, VCFHeader header) {

  if (!g.hasAnyAttribute(field)) {
    return false;
  }

  final VCFFormatHeaderLine metaData = header.getFormatHeaderLine(field);
  if (metaData == null) {
    logger.log(Level.WARNING, String.format("Could not find matching VCF header field for "
        + "genotype field %s", field));
    return false;
  }

  VCFHeaderLineType type = metaData.getType();
  Object value = g.getExtendedAttribute(field);
  final int fieldCount = metaData.getCount(vc);
  if (fieldCount == 1) {
    lvBuilder.addValues(createTypedValue(type, value));
    return true;
  }

  if (!(value instanceof String)) {
    throw new IllegalStateException("received non-Flag genotype field as non-String type");
  }
  String[] valueArray = ((String) value).split(",");
  if (valueArray.length == 1) {
    throw new IllegalStateException(String.format("header indicating a count greater than 1 "
        + "with non-List type found for field %s",
        field));
  }

  boolean allFalse = true;
  for (int i = 0; i < valueArray.length; i++) {
    VCFHeaderLineType thisType = VCFHeaderLineType.String;
    if (!valueArray[i].equals(VCFConstants.MISSING_VALUE_v4)) {
      thisType = type;
      allFalse = false;
    }

    lvBuilder.addValues(createTypedValue(thisType, valueArray[i]));
  }
  // We only add the lvBuilder if there is at least one non-missing value
  return !allFalse;
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
public void addHeadersInfixes(VCFHeader header, String prefix, String infix, String note) {
	VCFInfoHeaderLine infoDBSNPCommon = new VCFInfoHeaderLine(prefix + infix + "COMMON", VCFHeaderLineCount.A,
			VCFHeaderLineType.Integer,
			"Flagged as common in dbSNP" + note + ". Original description: RS is a common SNP.  A common SNP is "
					+ "one that has at least one 1000Genomes population with a minor allele "
					+ "of frequency >= 1% and for which 2 or more founders contribute to that minor allele "
					+ "frequency.");
	header.addMetaDataLine(infoDBSNPCommon);

	VCFInfoHeaderLine infoDBSNPFreqs = new VCFInfoHeaderLine(prefix + infix + "CAF", VCFHeaderLineCount.R,
			VCFHeaderLineType.Float,
			"Allele frequencies from dbSNP" + note + ". Original description: An ordered, comma delimited list "
					+ "of allele frequencies based on 1000Genomes, starting with the reference allele "
					+ "followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes "
					+ "alternate allele is not in the dbSNPs alternate allele set, the allele is added "
					+ "to the ALT column.  The minor allele is the second largest value in the list, "
					+ "and was previuosly reported in VCF as the GMAF.  This is the GMAF reported on "
					+ "the RefSNP and EntrezSNP pages and VariationReporter");
	header.addMetaDataLine(infoDBSNPFreqs);

	VCFInfoHeaderLine infoG5 = new VCFInfoHeaderLine(prefix + infix + "G5", VCFHeaderLineCount.A,
			VCFHeaderLineType.Integer, "Allele frequency >5% in all populations from dbSNP (yes: 1, no: 0)" + note
					+ ". Original description: >5% minor allele frequency in 1+ populations");
	header.addMetaDataLine(infoG5);

	VCFInfoHeaderLine infoG5A = new VCFInfoHeaderLine(prefix + infix + "G5A", VCFHeaderLineCount.A,
			VCFHeaderLineType.Integer, "Allele frequency >5% in all populations from dbSNP (yes: 1, no: 0)" + note
					+ ". Original description: >5% minor allele frequency in each and all populations");
	header.addMetaDataLine(infoG5A);

	if ("OVL_".equals(infix)) {
		VCFInfoHeaderLine overlappingRS = new VCFInfoHeaderLine(prefix + "OVL_IDS", VCFHeaderLineCount.A,
				VCFHeaderLineType.String, "dbSNP cluster identifiers with overlapping alternative positions, "
						+ "not necessarily matching alleles, for each alternative allele, separated '|'");
		header.addMetaDataLine(overlappingRS);
	} else {
		VCFInfoHeaderLine matchingRS = new VCFInfoHeaderLine(prefix + "IDS", VCFHeaderLineCount.A,
				VCFHeaderLineType.String,
				"dbSNP cluster identifiers with matching alternative positions and alleles, for each "
						+ "alternative alleles, separated by '|'");
		header.addMetaDataLine(matchingRS);
	}

	VCFInfoHeaderLine infoOrigin = new VCFInfoHeaderLine(prefix + infix + "SAO", VCFHeaderLineCount.A,
			VCFHeaderLineType.String, "Variant allele origin (UNSPECIFIED, GERMLINE, SOMATIC, BOTH)");
	header.addMetaDataLine(infoOrigin);
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
/** Add POPMAX name */
private void addPopmaxHeader(VCFHeader header, String prefix, String idInfix, String noteInfix) {
	VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "POPMAX", VCFHeaderLineCount.A,
			VCFHeaderLineType.String, "Population with the max AF" + noteInfix);
	header.addMetaDataLine(line);
}