Package htsjdk.variant.vcf

Class VCFContigHeaderLine

java.lang.Object

htsjdk.variant.vcf.VCFHeaderLine

htsjdk.variant.vcf.VCFSimpleHeaderLine

htsjdk.variant.vcf.VCFContigHeaderLine

All Implemented Interfaces:

VCFIDHeaderLine, Serializable, Comparable

public class VCFContigHeaderLine
extends VCFSimpleHeaderLine

A special class representing a contig VCF header line. Knows the true contig order and sorts on that Note: this class has a natural ordering that is inconsistent with equals()

See Also:

• Serialized Form

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFSimpleHeaderLine

DESCRIPTION_ATTRIBUTE, ID_ATTRIBUTE

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION

Constructor Summary

Constructors

Constructor	Description
VCFContigHeaderLine(String line, VCFHeaderVersion version, String key, int contigIndex)	create a VCF contig header line
VCFContigHeaderLine(Map<String,String> mapping, int contigIndex)

Method Summary

Modifier and Type	Method	Description
int	compareTo(Object other)	IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
boolean	equals(Object o)
Integer	getContigIndex()
SAMSequenceRecord	getSAMSequenceRecord()	Get the SAMSequenceRecord that corresponds to this VCF header line.
int	hashCode()

Methods inherited from class htsjdk.variant.vcf.VCFSimpleHeaderLine

getGenericFields, getID, initialize, toStringEncoding

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine

getKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncoding

Methods inherited from class java.lang.Object

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

Constructor Details

VCFContigHeaderLine

public VCFContigHeaderLine(String line,
 VCFHeaderVersion version,
 String key,
 int contigIndex)

create a VCF contig header line

Parameters:

line - the header line

version - the vcf header version

key - the key for this header line

VCFContigHeaderLine

public VCFContigHeaderLine(Map<String,String> mapping,
 int contigIndex)

Method Details

getContigIndex

public Integer getContigIndex()

getSAMSequenceRecord

public SAMSequenceRecord getSAMSequenceRecord()

Get the SAMSequenceRecord that corresponds to this VCF header line. If the VCF header line does not have a length tag, the SAMSequenceRecord returned will be set to have a length of SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTH. Records with unknown length will match any record with the same name when evaluated by SAMSequenceRecord.isSameSequence.

Returns:

The SAMSequenceRecord containing the ID, length, assembly, and index of this contig. Returns null if the contig header line does not have a length.

equals

public boolean equals(Object o)

Overrides:

equals in class VCFSimpleHeaderLine

hashCode

public int hashCode()

Overrides:

hashCode in class VCFSimpleHeaderLine

compareTo

public int compareTo(Object other)

IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER

Specified by:

compareTo in interface Comparable

Overrides:

compareTo in class VCFHeaderLine