Package picard.sam

Class AddCommentsToBam


@DocumentedFeature public class AddCommentsToBam extends CommandLineProgram
A tool to add comments to a BAM file header. Effectively copies the BAM file except for the addition of the @CO records in the header. This tool does not support SAM files. A block copying method is used to ensure efficient transfer to the output file.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="Input BAM file to add a comment to the header") public File INPUT
    • OUTPUT

      @Argument(shortName="O", doc="Output BAM file to write results") public File OUTPUT
    • COMMENT

      @Argument(shortName="C", doc="Comments to add to the BAM file") public List<String> COMMENT
  • Constructor Details

    • AddCommentsToBam

      public AddCommentsToBam()
  • Method Details

    • doWork

      protected int doWork()
      Description copied from class: CommandLineProgram
      Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
      Specified by:
      doWork in class CommandLineProgram
      Returns:
      program exit status.