pro.parseq.vcf.fields

Class Format

java.lang.Object

pro.parseq.vcf.types.VcfLine

pro.parseq.vcf.types.Metadata

pro.parseq.vcf.fields.Format

public class Format
extends Metadata

Represents VCF FORMAT meta-information field

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Constructor Summary

Constructors

Constructor and Description
Format(String line)

Method Summary

Modifier and Type	Method and Description
String	getDescription()
static Boolean	getGenotypeFieldValue(String value, int alleleNumber) Checks whether specified genotype contains particular allele
String	getId()
String	getNumber()
protected Pattern	getPattern()
FormatFieldType	getType()
List<? extends Serializable>	getValue(String value) Allows to extract field values from data lines
static boolean	isFormat(String line)
void	setDescription(String description)
void	setId(String id)
void	setNumber(String number)
void	setType(FormatFieldType type)

Methods inherited from class pro.parseq.vcf.types.Metadata

getKey, getValue

Methods inherited from class pro.parseq.vcf.types.VcfLine

isValid, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Format

public Format(String line)

Method Detail

getId

public String getId()

setId

public void setId(String id)

getNumber

public String getNumber()

setNumber

public void setNumber(String number)

getType

public FormatFieldType getType()

setType

public void setType(FormatFieldType type)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

getGenotypeFieldValue

public static final Boolean getGenotypeFieldValue(String value,
                                                  int alleleNumber)

Checks whether specified genotype contains particular allele

Parameters:

value - Genotype format field value (e.g. 0/1 or 1|2)

alleleNumber - VCF data line allele number (0 for reference allele, 1,2.. for alternates)

Returns:

Whether allele is in the genotype or null of value is malformed

getValue

public List<? extends Serializable> getValue(String value)

Allows to extract field values from data lines

Parameters:

value - Data line FORMAT value from samples' details specified for the field

Returns:

List of found values (see VCFv4.2 specification for more details)

getPattern

protected Pattern getPattern()

Overrides:

getPattern in class Metadata

isFormat

public static final boolean isFormat(String line)