pro.parseq.vcf.types

Class Variant

java.lang.Object

pro.parseq.vcf.types.Variant

public class Variant
extends Object

Class to hold an information about single genetic variant from VCF data line

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Constructor Summary

Constructors

Constructor and Description
Variant()

Method Summary

Modifier and Type	Method and Description
boolean	addFilter(Filter filter)
boolean	addId(String id)
int	getAllele()
String	getAlt()
String	getChrom()
List<Filter>	getFilters()
Map<String,Map<String,List<? extends Serializable>>>	getFormats()
Map<String,Genotype>	getGenotypes()
List<String>	getIds()
Map<String,List<? extends Serializable>>	getInfo()
long	getPos()
Double	getQual()
String	getRef()
Genotype	getZygosityFor(String sampleName)
boolean	isFiltered()
boolean	isFoundVariantFor(String sampleName)
Map<String,List<? extends Serializable>>	putFormat(String sampleName, Map<String,List<? extends Serializable>> format)
Genotype	putGenotype(String sampleName, Genotype zygosity)
List<? extends Serializable>	putInfo(String key, List<? extends Serializable> value)
void	setAllele(int allele)
void	setAlt(String alt)
void	setChrom(String chrom)
void	setFiltered(boolean filtered)
void	setFilters(List<Filter> filters)
void	setFormats(Map<String,Map<String,List<? extends Serializable>>> formats)
void	setGenotypes(Map<String,Genotype> genotypes)
void	setIds(List<String> ids)
void	setInfo(Map<String,List<? extends Serializable>> info)
void	setPos(long pos)
void	setQual(Double qual)
void	setRef(String ref)

Methods inherited from class java.lang.Object

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

Constructor Detail

Variant

public Variant()

Method Detail

getChrom

public String getChrom()

setChrom

public void setChrom(String chrom)

getPos

public long getPos()

setPos

public void setPos(long pos)

getIds

public List<String> getIds()

addId

public boolean addId(String id)

setIds

public void setIds(List<String> ids)

getRef

public String getRef()

setRef

public void setRef(String ref)

getAlt

public String getAlt()

setAlt

public void setAlt(String alt)

getQual

public Double getQual()

setQual

public void setQual(Double qual)

isFiltered

public boolean isFiltered()

setFiltered

public void setFiltered(boolean filtered)

getFilters

public List<Filter> getFilters()

addFilter

public boolean addFilter(Filter filter)

setFilters

public void setFilters(List<Filter> filters)

getInfo

public Map<String,List<? extends Serializable>> getInfo()

putInfo

public List<? extends Serializable> putInfo(String key,
                                            List<? extends Serializable> value)

setInfo

public void setInfo(Map<String,List<? extends Serializable>> info)

getFormats

public Map<String,Map<String,List<? extends Serializable>>> getFormats()

putFormat

public Map<String,List<? extends Serializable>> putFormat(String sampleName,
                                                          Map<String,List<? extends Serializable>> format)

setFormats

public void setFormats(Map<String,Map<String,List<? extends Serializable>>> formats)

getAllele

public int getAllele()

setAllele

public void setAllele(int allele)

getGenotypes

public Map<String,Genotype> getGenotypes()

putGenotype

public Genotype putGenotype(String sampleName,
                            Genotype zygosity)

setGenotypes

public void setGenotypes(Map<String,Genotype> genotypes)

getZygosityFor

public Genotype getZygosityFor(String sampleName)

isFoundVariantFor

public boolean isFoundVariantFor(String sampleName)