Class CollectWgsMetricsWithNonZeroCoverage


  • @DocumentedFeature
    @ExperimentalFeature
    public class CollectWgsMetricsWithNonZeroCoverage
    extends CollectWgsMetrics
    • Field Detail

      • CHART_OUTPUT

        @Argument(shortName="CHART",
                  doc="A file (with .pdf extension) to write the chart to.")
        public File CHART_OUTPUT
    • Constructor Detail

      • CollectWgsMetricsWithNonZeroCoverage

        public CollectWgsMetricsWithNonZeroCoverage()
    • 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.
      • getSamReader

        protected htsjdk.samtools.SamReader getSamReader()
        Description copied from class: CollectWgsMetrics
        Gets the SamReader from which records will be examined. This will also set the header so that it is available in
        Overrides:
        getSamReader in class CollectWgsMetrics
      • 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.
        Overrides:
        doWork in class CollectWgsMetrics
        Returns:
        program exit status.
      • generateWgsMetrics

        protected WgsMetrics generateWgsMetrics​(htsjdk.samtools.util.IntervalList intervals,
                                                htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
                                                htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
                                                double pctExcludedByAdapter,
                                                double pctExcludedByMapq,
                                                double pctExcludedByDupes,
                                                double pctExcludedByPairing,
                                                double pctExcludedByBaseq,
                                                double pctExcludedByOverlap,
                                                double pctExcludedByCapping,
                                                double pctTotal,
                                                int coverageCap,
                                                htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram,
                                                int sampleSize)
        Overrides:
        generateWgsMetrics in class CollectWgsMetrics