Class VCFContigHeaderLine

    • 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()
        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.