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.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

All Methods Instance Methods Concrete Methods
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()`
`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 Detail

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 Detail
- getContigIndex
```
public Integer getContigIndex()
```
- getSAMSequenceRecord
```
public SAMSequenceRecord getSAMSequenceRecord()
```
- 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

Class VCFContigHeaderLine

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

Constructor Summary

Method Summary

Methods inherited from class htsjdk.variant.vcf.VCFSimpleHeaderLine

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine

Methods inherited from class java.lang.Object

Constructor Detail

VCFContigHeaderLine

VCFContigHeaderLine

Method Detail

getContigIndex

getSAMSequenceRecord

equals

hashCode

compareTo