Class CollectIlluminaLaneMetrics

    • Field Detail

      • RUN_DIRECTORY

        @Argument(doc="The Illumina run directory of the run for which the lane metrics are to be generated")
        public File RUN_DIRECTORY
      • OUTPUT_DIRECTORY

        @Argument(doc="The directory to which the output file will be written")
        public File OUTPUT_DIRECTORY
      • OUTPUT_PREFIX

        @Argument(doc="The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied",
                  shortName="O")
        public String OUTPUT_PREFIX
      • READ_STRUCTURE

        @Argument(doc="A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the  data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip).  E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein.\nIf not given, will use the RunInfo.xml in the run directory.",
                  shortName="RS",
                  optional=true)
        public ReadStructure READ_STRUCTURE
      • FILE_EXTENSION

        @Argument(shortName="EXT",
                  doc="Append the given file extension to all metric file names (ex. OUTPUT.illumina_lane_metrics.EXT). None if null",
                  optional=true)
        public String FILE_EXTENSION
      • IS_NOVASEQ

        @Argument(doc="Boolean the determines if this run is a NovaSeq run or not. (NovaSeq tile metrics files are in cycle 25 directory.",
                  optional=true)
        public boolean IS_NOVASEQ
    • Constructor Detail

      • CollectIlluminaLaneMetrics

        public CollectIlluminaLaneMetrics()
    • Method Detail

      • 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.
      • main

        public static void main​(String[] args)