Class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection

java.lang.Object
picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
All Implemented Interfaces:
ReferenceArgumentCollection
Enclosing class:
CollectAlignmentSummaryMetrics

public static class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection extends Object implements ReferenceArgumentCollection
  • Field Details

    • REFERENCE_SEQUENCE

      @Argument(shortName="R", doc="Reference sequence file. Note that while this argument isn\'t required, without it a small subset (MISMATCH-related) of the metrics cannot be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.", optional=true) public File REFERENCE_SEQUENCE
  • Constructor Details

    • CollectAlignmentRefArgCollection

      public CollectAlignmentRefArgCollection()
  • 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.