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 PicardHtsPath REFERENCE_SEQUENCE
  • Constructor Details

    • OptionalReferenceArgumentCollection

      public OptionalReferenceArgumentCollection()
  • Method Details

    • getReferenceFile

      public File getReferenceFile()
      Description copied from interface: ReferenceArgumentCollection
      This method is retained for backward compatibility with legacy tools that have not been updated to support PicardHtsPath input files. The preferred methods for accessing the reference file provided on the command line is either getHtsPath() or getReferencePath(). TODO: update tools that call this method to use getHtsPath()
      Specified by:
      getReferenceFile in interface ReferenceArgumentCollection
      Returns:
      The reference provided by the user, or the default defined by htsjdk.samtools.Defaults.REFERENCE_FASTA. May be null.
    • getReferencePath

      public Path getReferencePath()
      Description copied from interface: ReferenceArgumentCollection
      This method first checks if the PicardHtsPath is null, thereby avoiding NPE that results from getHtsPath.toPath(). Use this for providing input to methods that expect the Path to be null when the reference is absent e.g. SamReaderFactory.referenceSequence().
      Specified by:
      getReferencePath in interface ReferenceArgumentCollection
      Returns:
      The reference provided by the user or the default as an nio Path. May be null.
    • getHtsPath

      public PicardHtsPath getHtsPath()
      Description copied from interface: ReferenceArgumentCollection
      Returns a PicardHtsPath for the reference input. Maybe be null. Implementers of this interface should override with an appropriate implementation. This currently does not support remote paths set via HtsJdk.Defaults.REFERENCE_FASTA, since that uses a `File` object.
      Specified by:
      getHtsPath in interface ReferenceArgumentCollection
      Returns:
      The reference provided by the user, if any, or the default, if any, as a PicardHtsPath. May be null.