Class OptionalReferenceArgumentCollection

    • Field Detail

      • REFERENCE_SEQUENCE

        @Argument(shortName="R",
                  doc="Reference sequence file.",
                  common=true,
                  optional=true)
        public File REFERENCE_SEQUENCE
    • Constructor Detail

      • OptionalReferenceArgumentCollection

        public OptionalReferenceArgumentCollection()
    • Method Detail

      • getReferenceFile

        public File getReferenceFile()
        Specified by:
        getReferenceFile in interface ReferenceArgumentCollection
        Returns:
        The reference provided by the user, if any, or the default defined by htsjdk.samtools.Defaults.REFERENCE_FASTA