org.molgenis.vcf

Class VcfRecord

java.lang.Object

org.molgenis.vcf.VcfRecord

public class VcfRecord
extends Object

Constructor Summary

Constructors

Constructor and Description
VcfRecord(VcfMeta vcfMeta)
VcfRecord(VcfMeta vcfMeta, String[] tokens)

Method Summary

Modifier and Type	Method and Description
VcfRecord	createClone()
boolean	equals(Object obj)
List<Allele>	getAlternateAlleles()
String	getChromosome()
String	getFilterStatus()
String[]	getFormat()
int	getFormatIndex(String dataType)
List<String>	getIdentifiers()
Iterable<VcfInfo>	getInformation()
int	getNrSamples()
int	getPosition()
String	getQuality()
Allele	getReferenceAllele()
Iterable<VcfSample>	getSamples()
String[]	getTokens()
VcfMeta	getVcfMeta()
int	hashCode()
void	reset(String[] tokens)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

VcfRecord

public VcfRecord(VcfMeta vcfMeta)

VcfRecord

public VcfRecord(VcfMeta vcfMeta,
                 String[] tokens)

Method Detail

getTokens

public String[] getTokens()

getChromosome

public String getChromosome()

getPosition

public int getPosition()

getIdentifiers

public List<String> getIdentifiers()

getReferenceAllele

public Allele getReferenceAllele()

getAlternateAlleles

public List<Allele> getAlternateAlleles()

Returns:

list of alternate alleles or empty list if alternate alleles string is set to the missing value

getQuality

public String getQuality()

Returns:

quality value or null if quality value is set to the missing value

getFilterStatus

public String getFilterStatus()

Returns:

filter status or null if filter status is set to the missign value

getInformation

public Iterable<VcfInfo> getInformation()

getFormat

public String[] getFormat()

getFormatIndex

public int getFormatIndex(String dataType)

getNrSamples

public int getNrSamples()

getSamples

public Iterable<VcfSample> getSamples()

getVcfMeta

public VcfMeta getVcfMeta()

reset

public void reset(String[] tokens)

createClone

public VcfRecord createClone()

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object