Package org.broadinstitute.hellbender.tools.funcotator.metadata

Class VcfFuncotationMetadata

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata

All Implemented Interfaces:

FuncotationMetadata

public class VcfFuncotationMetadata
extends Object
implements FuncotationMetadata

A concrete class for FuncotationMetadata that can be easily built from a VCF Header.

Method Summary

Modifier and Type	Method	Description
static VcfFuncotationMetadata	create(List<htsjdk.variant.vcf.VCFInfoHeaderLine> vcfInfoHeaderLines)
boolean	equals(Object o)
int	hashCode()
List<htsjdk.variant.vcf.VCFInfoHeaderLine>	retrieveAllHeaderInfo()	See FuncotationMetadata.retrieveAllHeaderInfo()
htsjdk.variant.vcf.VCFInfoHeaderLine	retrieveHeaderInfo(String fieldName)	See FuncotationMetadata.retrieveHeaderInfo(String)
String	toString()

Methods inherited from class java.lang.Object

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

Method Details

create

public static VcfFuncotationMetadata create(List<htsjdk.variant.vcf.VCFInfoHeaderLine> vcfInfoHeaderLines)

Parameters:

vcfInfoHeaderLines - Never null

Returns:

Metadata corresponding to VCF info fields. Never null

retrieveHeaderInfo

public htsjdk.variant.vcf.VCFInfoHeaderLine retrieveHeaderInfo(String fieldName)

See FuncotationMetadata.retrieveHeaderInfo(String)

Specified by:

retrieveHeaderInfo in interface FuncotationMetadata

Parameters:

fieldName - field to search. Never null

Returns:

Never null

retrieveAllHeaderInfo

public List<htsjdk.variant.vcf.VCFInfoHeaderLine> retrieveAllHeaderInfo()

See FuncotationMetadata.retrieveAllHeaderInfo()

Specified by:

retrieveAllHeaderInfo in interface FuncotationMetadata

Returns:

Never null

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object