Package picard.sam

Class CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection

java.lang.Object
picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
All Implemented Interfaces:
ReferenceArgumentCollection
Enclosing class:
CreateSequenceDictionary

public static class CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection extends Object implements ReferenceArgumentCollection
  • Field Details

    • REFERENCE

      @Argument(doc="Input reference fasta or fasta.gz", shortName="R") public PicardHtsPath REFERENCE
  • Constructor Details

    • CreateSeqDictReferenceArgumentCollection

      public CreateSeqDictReferenceArgumentCollection()
  • Method Details

    • 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.
    • 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.