Package picard.sam

Class ReplaceSamHeader

    • Field Detail

      • INPUT

        @Argument(doc="SAM/BAM/CRAM file from which SAMRecords will be read.",
                  shortName="I")
        public File INPUT
      • HEADER

        @Argument(doc="SAM/BAM/CRAM file from which SAMFileHeader will be read.")
        public File HEADER
      • OUTPUT

        @Argument(doc="header from HEADER file will be written to this file, followed by records from INPUT file",
                  shortName="O")
        public File OUTPUT
    • Constructor Detail

      • ReplaceSamHeader

        public ReplaceSamHeader()
    • Method Detail

      • doWork

        protected int doWork()
        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.