Package picard.analysis

Class CollectWgsMetricsWithNonZeroCoverage

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.CollectWgsMetrics
picard.analysis.CollectWgsMetricsWithNonZeroCoverage
@DocumentedFeature @ExperimentalFeature public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics

  • Field Details

    • CHART_OUTPUT

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

  • Constructor Details

    • CollectWgsMetricsWithNonZeroCoverage

      public CollectWgsMetricsWithNonZeroCoverage()

  • 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.

    • 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

    • getCollector

      protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
      Description copied from class: CollectWgsMetrics
      Creates AbstractWgsMetricsCollector implementation according to CollectWgsMetrics.USE_FAST_ALGORITHM value.
      Overrides:
      getCollector in class CollectWgsMetrics
      Parameters:
      coverageCap - the maximum depth/coverage to consider.
      intervals - the intervals over which metrics are collected.
      Returns:
      if CollectWgsMetrics.USE_FAST_ALGORITHM is enabled, returns FastWgsMetricsCollector implementation, otherwise default algorithm is used and CollectWgsMetrics.WgsMetricsCollector is returned.