htsjdk.variant.vcf

Class VCFContigHeaderLine

java.lang.Object

htsjdk.variant.vcf.VCFHeaderLine

htsjdk.variant.vcf.VCFSimpleHeaderLine

htsjdk.variant.vcf.VCFContigHeaderLine

All Implemented Interfaces:

VCFIDHeaderLine, java.lang.Comparable

public class VCFContigHeaderLine
extends VCFSimpleHeaderLine

A special class representing a contig VCF header line. Knows the true contig order and sorts on that

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

ALLOW_UNBOUND_DESCRIPTIONS, UNBOUND_DESCRIPTION

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(java.lang.Object other) IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
java.lang.Integer	getContigIndex()
SAMSequenceRecord	getSAMSequenceRecord()

Methods inherited from class htsjdk.variant.vcf.VCFSimpleHeaderLine

equals, 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, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

VCFContigHeaderLine

public VCFContigHeaderLine(java.lang.String line,
                   VCFHeaderVersion version,
                   java.lang.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(java.util.Map<java.lang.String,java.lang.String> mapping,
                   int contigIndex)

Method Detail

getContigIndex

public java.lang.Integer getContigIndex()

getSAMSequenceRecord

public SAMSequenceRecord getSAMSequenceRecord()

compareTo

public int compareTo(java.lang.Object other)

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

Specified by:

compareTo in interface java.lang.Comparable

Overrides:

compareTo in class VCFHeaderLine