public class VCFContigHeaderLine extends VCFSimpleHeaderLine
ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION| 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
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| 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
|
boolean |
equals(java.lang.Object o) |
java.lang.Integer |
getContigIndex() |
SAMSequenceRecord |
getSAMSequenceRecord() |
int |
hashCode() |
getID, initialize, toStringEncodinggetKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncodingpublic 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 VCFSimpleHeaderLinepublic int hashCode()
hashCode in class VCFSimpleHeaderLinepublic int compareTo(java.lang.Object other)
compareTo in interface java.lang.ComparablecompareTo in class VCFHeaderLine