public class VCFContigHeaderLine extends VCFSimpleHeaderLine
DESCRIPTION_ATTRIBUTE, ID_ATTRIBUTE
ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION
Constructor and Description |
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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
|
Modifier and Type | Method and Description |
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int |
compareTo(java.lang.Object other)
IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
|
boolean |
equals(java.lang.Object o) |
java.lang.Integer |
getContigIndex() |
SAMSequenceRecord |
getSAMSequenceRecord() |
int |
hashCode() |
getGenericFields, getID, initialize, toStringEncoding
getKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncoding
public VCFContigHeaderLine(java.lang.String line, VCFHeaderVersion version, java.lang.String key, int contigIndex)
line
- the header lineversion
- the vcf header versionkey
- the key for this header linepublic VCFContigHeaderLine(java.util.Map<java.lang.String,java.lang.String> mapping, int contigIndex)
public java.lang.Integer getContigIndex()
public SAMSequenceRecord getSAMSequenceRecord()
public boolean equals(java.lang.Object o)
equals
in class VCFSimpleHeaderLine
public int hashCode()
hashCode
in class VCFSimpleHeaderLine
public int compareTo(java.lang.Object other)
compareTo
in interface java.lang.Comparable
compareTo
in class VCFHeaderLine