Package picard.sam

Class CalculateReadGroupChecksum

java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.CalculateReadGroupChecksum

@DocumentedFeature public class CalculateReadGroupChecksum extends CommandLineProgram
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="The input SAM or BAM file. ") public File INPUT
    • OUTPUT

      @Argument(shortName="O", doc="The file to which the hash code should be written.", optional=true) public File OUTPUT
  • Constructor Details

    • CalculateReadGroupChecksum

      public CalculateReadGroupChecksum()
  • Method Details

    • getOutputFileName

      public static String getOutputFileName(File inputFile)
      Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
    • 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.