Java VCFHeaderLineType.Float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
private String getGroupByField(List<VcfFile> files, String groupBy) throws IOException {
    IndexSortField sortField = IndexSortField.getByName(groupBy);
    if (sortField == null) {
        VcfFilterInfo info = vcfManager.getFiltersInfo(
            files.stream().map(BaseEntity::getId).collect(Collectors.toList()));

        InfoItem infoItem = info.getInfoItemMap().get(groupBy);
        Assert.notNull(infoItem, "Unknown sort field: " + groupBy);

        if (infoItem.getType() == VCFHeaderLineType.Integer || infoItem.getType() == VCFHeaderLineType.Float) {
            return FeatureIndexFields.getGroupName(infoItem.getName().toLowerCase());
        } else {
            return infoItem.getName().toLowerCase();
        }
    } else {
        if (sortField.getType() == SortField.Type.INT || sortField.getType() == SortField.Type.FLOAT) {
            return sortField.getField().getGroupName();
        } else {
            return sortField.getField().fieldName;
        }
    }
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
private static Value createTypedValue(VCFHeaderLineType type, Object value) {
  if (type == VCFHeaderLineType.Flag) {
    return Value.newBuilder().setBoolValue((Boolean) value).build();
  }

  // Booleans are given as Boolean objects. Strangely, Floats and Integers
  // are given as String objects by HTSJDK.
  if (!(value instanceof String)) {
    throw new IllegalStateException("Received non-Boolean, non-List type in non-String format. "
        + "This is most likely due to a change in htsjdk's library.");
  }

  String stringValue = (String) value;
  boolean isNumeric = stringValue.matches("[-+]?\\d+(\\.\\d+)?");

  if (type == VCFHeaderLineType.Integer && isNumeric) {
    return Value.newBuilder().setNumberValue(Integer.parseInt(stringValue)).build();
  }

  if (type == VCFHeaderLineType.Float && isNumeric) {
    return Value.newBuilder().setNumberValue(Double.parseDouble(stringValue)).build();
  }


  return Value.newBuilder().setStringValue(stringValue).build();
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
private String getGroupByField(List<VcfFile> files, String groupBy) throws IOException {
    IndexSortField sortField = IndexSortField.getByName(groupBy);
    if (sortField == null) {
        VcfFilterInfo info = vcfManager.getFiltersInfo(
                files.stream().map(BaseEntity::getId).collect(Collectors.toList()));

        InfoItem infoItem = info.getInfoItemMap().get(groupBy);
        Assert.notNull(infoItem, "Unknown sort field: " + groupBy);

        if (infoItem.getType() == VCFHeaderLineType.Integer || infoItem.getType() == VCFHeaderLineType.Float) {
            return FeatureIndexFields.getGroupName(infoItem.getName().toLowerCase());
        } else {
            return infoItem.getName().toLowerCase();
        }
    } else {
        if (sortField.getType() == SortField.Type.INT || sortField.getType() == SortField.Type.FLOAT) {
            return sortField.getField().getGroupName();
        } else {
            return sortField.getField().fieldName;
        }
    }
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
/** Add header with allele frequency */
private void addAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ExacPopulation pop) {
	String popName;
	if (pop == ExacPopulation.ALL)
		popName = "all populations";
	else
		popName = pop + " / " + pop.getLabel() + " population";
	VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_" + pop, VCFHeaderLineCount.A,
			VCFHeaderLineType.Float, "Frequency observed in ExAC data set in " + popName + noteInfix);
	header.addMetaDataLine(line);
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
/** Add header with allele frequency */
private void addAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, GnomadPopulation pop) {
	String popName;
	if (pop == GnomadPopulation.ALL)
		popName = "all populations";
	else
		popName = pop + " / " + pop.getLabel() + " population";
	VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_" + pop, VCFHeaderLineCount.A,
			VCFHeaderLineType.Float, "Frequency observed in ExAC data set in " + popName + noteInfix);
	header.addMetaDataLine(line);
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
FamilyInfo(final Pedigree.Family pedFamily)
{
this.pedFamily=pedFamily;
final String prefix=
		(
		StringUtil.isBlank(CtxWriterFactory.this.prefix)?
		CtxWriterFactory.this.prefix+"_":""
		)+
	this.pedFamily.getId()
	;
this.ac = new VCFInfoHeaderLine(
		prefix+"_AC",
		VCFHeaderLineCount.A,
		VCFHeaderLineType.Integer,
		"Number of alleles carrying the variant allele for the family "+this.pedFamily.getId()
		);
this.an = new VCFInfoHeaderLine(
		prefix+"_AN",
		1,
		VCFHeaderLineType.Integer,
		"Number of alleles for the family "+this.pedFamily.getId()
		);
this.af = new VCFInfoHeaderLine(
		prefix+"_AF",
		VCFHeaderLineCount.A,
		VCFHeaderLineType.Float,
		"Allele Frequency for the family "+this.pedFamily.getId()
		);
}
 

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 header for highest allele frequency */
private void addBestAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix) {
	VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_POPMAX", VCFHeaderLineCount.A,
			VCFHeaderLineType.Float, "Highest allele frequency seen in any population" + noteInfix);
	header.addMetaDataLine(line);
}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
@Override
public void writeHeader(final VCFHeader header)
	{
	final VCFHeader h2= new VCFHeader(header);
	
	this.filter = new VCFFilterHeaderLine("BurdenExac",
				"Freq:"+CtxWriterFactory.this.maxFreq+" Pop:"+CtxWriterFactory.this.exacPopulationStr);
	h2.addMetaDataLine(this.filter);
		
	this.freqExacInfoHeader = new VCFInfoHeaderLine(
			"FreqExac",
			VCFHeaderLineCount.A,
			VCFHeaderLineType.Float,
			"Freq in Exac AC/AN"
			);
	h2.addMetaDataLine(freqExacInfoHeader);
	
	
	for(final String pop:exacPopulations)
		{
		if(pop.isEmpty()) continue;
		final VCFInfoHeaderLine ac = exacHeader.getInfoHeaderLine("AC_"+pop);
		if(ac==null) 
			{
			throw new JvarkitException.FileFormatError("Cannot find AC_"+pop+" in "+CtxWriterFactory.this.exacFile+" header");
			}
		if(ac.getCountType()!=VCFHeaderLineCount.A)
			{
			throw new JvarkitException.FileFormatError("expected VCFHeaderLineCount.A for "+ac );
			}
		h2.addMetaDataLine(ac);
		final VCFInfoHeaderLine an = exacHeader.getInfoHeaderLine("AN_"+pop);
		if(an==null)
			{
			throw new JvarkitException.FileFormatError("Cannot find AN_"+pop+" in "+CtxWriterFactory.this.exacFile+" header");
			}
		if(an.getCount()!=1)
			{
			throw new JvarkitException.FileFormatError("expected getCount==1 for "+an );
			}
		h2.addMetaDataLine(an);
		}
	super.writeHeader(h2);
	}
 

import htsjdk.variant.vcf.VCFHeaderLineType; //导入方法依赖的package包/类
KeyAndType(final String key)
{
this(key,VCFHeaderLineCount.A,VCFHeaderLineType.Float);
}