Class CollectHiSeqXPfFailMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.illumina.quality.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 Details

    • 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
    • detailedMetricsExtension

      public static final String detailedMetricsExtension
      See Also:
    • summaryMetricsExtension

      public static final String summaryMetricsExtension
      See Also:
  • Constructor Details

    • CollectHiSeqXPfFailMetrics

      public CollectHiSeqXPfFailMetrics()
  • Method Details

    • 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.