Package picard.sam

Class CalculateReadGroupChecksum

    • Field Detail

      • 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 Detail

      • CalculateReadGroupChecksum

        public CalculateReadGroupChecksum()
    • Method Detail

      • main

        public static void main​(String[] args)
      • 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.