Package picard.util

Class ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection

java.lang.Object
picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
All Implemented Interfaces:
ReferenceArgumentCollection
Enclosing class:
ScatterIntervalsByNs

public static class ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection extends Object implements ReferenceArgumentCollection
  • Field Details

    • REFERENCE

      @Argument(shortName="R", doc="Reference sequence to use. Note: this tool requires that the reference fasta has both an associated index and a dictionary.") public File REFERENCE
  • Constructor Details

    • ScatterIntervalsByNReferenceArgumentCollection

      public ScatterIntervalsByNReferenceArgumentCollection()
  • 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.