Class OptionalReferenceArgumentCollection

java.lang.Object
picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
All Implemented Interfaces:
ReferenceArgumentCollection

public class OptionalReferenceArgumentCollection extends Object implements ReferenceArgumentCollection
Picard default argument collection for an optional reference.
  • Field Details

    • REFERENCE_SEQUENCE

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

    • OptionalReferenceArgumentCollection

      public OptionalReferenceArgumentCollection()
  • Method Details

    • 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