Package picard.illumina.quality

Class CollectHiSeqXPfFailMetrics

  • @DocumentedFeature
public class CollectHiSeqXPfFailMetrics
extends CommandLineProgram
    Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter. (BETA)

    • Field Detail

      • BASECALLS_DIR

        @Argument(doc="The Illumina basecalls directory. ",
          shortName="B")
public File BASECALLS_DIR

      • OUTPUT

        @Argument(shortName="O",
          doc="Basename for metrics file. Resulting file will be <OUTPUT>.pffail_summary_metrics",
          optional=false)
public File OUTPUT

      • PROB_EXPLICIT_READS

        @Argument(shortName="P",
          doc="The fraction of (non-PF) reads for which to output explicit classification. Output file will be <OUTPUT>.pffail_detailed_metrics (if PROB_EXPLICIT_READS != 0)",
          optional=true)
public double PROB_EXPLICIT_READS

      • LANE

        @Argument(doc="Lane number.",
          shortName="L")
public Integer LANE

      • NUM_PROCESSORS

        @Argument(shortName="NP",
          doc="Run this many PerTileBarcodeExtractors in parallel.  If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.",
          optional=true)
public int NUM_PROCESSORS

      • N_CYCLES

        @Argument(doc="Number of cycles to look at. At time of writing PF status gets determined at cycle 24 so numbers greater than this will yield strange results. In addition, PF status is currently determined at cycle 24, so running this with any other value is neither tested nor recommended.",
          optional=true)
public int N_CYCLES

    • Constructor Detail

      • CollectHiSeqXPfFailMetrics

        public CollectHiSeqXPfFailMetrics()

    • Method Detail

      • customCommandLineValidation

        protected String[] customCommandLineValidation()
        Description copied from class: CommandLineProgram
        Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
        Overrides:
        customCommandLineValidation in class CommandLineProgram
        Returns:
        null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

      • 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.