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

      • main

        public static void main​(String[] args)
      • 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 CollectWgsMetrics.WgsMetrics generateWgsMetrics​(htsjdk.samtools.util.IntervalList intervals,
                                                                  htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
                                                                  htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
                                                                  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