htsjdk.variant.vcf

Class VCFCompoundHeaderLine

java.lang.Object

htsjdk.variant.vcf.VCFHeaderLine

htsjdk.variant.vcf.VCFCompoundHeaderLine

All Implemented Interfaces:

VCFIDHeaderLine, java.io.Serializable, java.lang.Comparable

Direct Known Subclasses:

VCFFormatHeaderLine, VCFInfoHeaderLine

public abstract class VCFCompoundHeaderLine
extends VCFHeaderLine
implements VCFIDHeaderLine

a base class for compound header lines, which include info lines and format lines (so far)

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VCFCompoundHeaderLine.SupportedHeaderLineType

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	VCFCompoundHeaderLine(java.lang.String name, int count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType) create a VCF format header line
protected	VCFCompoundHeaderLine(java.lang.String name, int count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType, java.lang.String source, java.lang.String version) create a VCF format header line
protected	VCFCompoundHeaderLine(java.lang.String name, VCFHeaderLineCount count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType) create a VCF format header line
protected	VCFCompoundHeaderLine(java.lang.String name, VCFHeaderLineCount count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType, java.lang.String source, java.lang.String version) create a VCF format header line
protected	VCFCompoundHeaderLine(java.lang.String line, VCFHeaderVersion version, VCFCompoundHeaderLine.SupportedHeaderLineType lineType) create a VCF format header line

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o) returns true if we're equal to another compound header line
boolean	equalsExcludingDescription(VCFCompoundHeaderLine other)
int	getCount()
int	getCount(VariantContext vc) Get the number of values expected for this header field, given the properties of VariantContext vc If the count is a fixed count, return that.
VCFHeaderLineCount	getCountType()
java.lang.String	getDescription()
java.lang.String	getID()
java.lang.String	getSource()
VCFHeaderLineType	getType()
java.lang.String	getVersion()
int	hashCode()
boolean	isFixedCount()
boolean	sameLineTypeAndName(VCFCompoundHeaderLine other)
void	setNumberToUnbounded()
void	setSource(java.lang.String source) Specify annotation source
void	setVersion(java.lang.String version) Specify annotation version
protected java.lang.String	toStringEncoding() make a string representation of this header line

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine

compareTo, getKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncoding

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFCompoundHeaderLine

protected VCFCompoundHeaderLine(java.lang.String name,
                                int count,
                                VCFHeaderLineType type,
                                java.lang.String description,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType)

create a VCF format header line

Parameters:

name - the name for this header line

count - the count for this header line

type - the type for this header line

description - the description for this header line

lineType - the header line type

VCFCompoundHeaderLine

protected VCFCompoundHeaderLine(java.lang.String name,
                                VCFHeaderLineCount count,
                                VCFHeaderLineType type,
                                java.lang.String description,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType)

create a VCF format header line

Parameters:

name - the name for this header line

count - the count type for this header line

type - the type for this header line

description - the description for this header line

lineType - the header line type

VCFCompoundHeaderLine

protected VCFCompoundHeaderLine(java.lang.String name,
                                int count,
                                VCFHeaderLineType type,
                                java.lang.String description,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType,
                                java.lang.String source,
                                java.lang.String version)

create a VCF format header line

Parameters:

name - the name for this header line

count - the count for this header line

type - the type for this header line

description - the description for this header line

lineType - the header line type

source - annotation source (case-insensitive, e.g. "dbsnp")

version - exact version (e.g. "138")

VCFCompoundHeaderLine

protected VCFCompoundHeaderLine(java.lang.String name,
                                VCFHeaderLineCount count,
                                VCFHeaderLineType type,
                                java.lang.String description,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType,
                                java.lang.String source,
                                java.lang.String version)

create a VCF format header line

Parameters:

name - the name for this header line

count - the count type for this header line

type - the type for this header line

description - the description for this header line

lineType - the header line type

source - annotation source (case-insensitive, e.g. "dbsnp")

version - exact version (e.g. "138")

VCFCompoundHeaderLine

protected VCFCompoundHeaderLine(java.lang.String line,
                                VCFHeaderVersion version,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType)

create a VCF format header line

Parameters:

line - the header line

version - the VCF header version

lineType - the header line type

Method Detail

getID

public java.lang.String getID()

Specified by:

getID in interface VCFIDHeaderLine

getDescription

public java.lang.String getDescription()

getType

public VCFHeaderLineType getType()

getCountType

public VCFHeaderLineCount getCountType()

isFixedCount

public boolean isFixedCount()

getCount

public int getCount()

getSource

public java.lang.String getSource()

getVersion

public java.lang.String getVersion()

getCount

public int getCount(VariantContext vc)

Get the number of values expected for this header field, given the properties of VariantContext vc If the count is a fixed count, return that. For example, a field with size of 1 in the header returns 1 If the count is of type A, return vc.getNAlleles - 1 If the count is of type R, return vc.getNAlleles If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information at all, then implicitly assume diploid samples when computing G values. If the count is UNBOUNDED return -1

Parameters:

vc -

Returns:

setNumberToUnbounded

public void setNumberToUnbounded()

toStringEncoding

protected java.lang.String toStringEncoding()

make a string representation of this header line

Overrides:

toStringEncoding in class VCFHeaderLine

Returns:

a string representation

equals

public boolean equals(java.lang.Object o)

returns true if we're equal to another compound header line

Overrides:

equals in class VCFHeaderLine

Parameters:

o - a compound header line

Returns:

true if equal

hashCode

public int hashCode()

Overrides:

hashCode in class VCFHeaderLine

equalsExcludingDescription

public boolean equalsExcludingDescription(VCFCompoundHeaderLine other)

sameLineTypeAndName

public boolean sameLineTypeAndName(VCFCompoundHeaderLine other)

setSource

public void setSource(java.lang.String source)

Specify annotation source

This value is optional starting with VCFv4.2.

Parameters:

source - annotation source (case-insensitive, e.g. "dbsnp")

setVersion

public void setVersion(java.lang.String version)

Specify annotation version

This value is optional starting with VCFv4.2.

Parameters:

version - exact version (e.g. "138")