Class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

java.lang.Object
picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
picard.analysis.CollectWgsMetrics.WgsMetricsCollector
picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
Enclosing class:
CollectWgsMetricsWithNonZeroCoverage

protected class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector extends CollectWgsMetrics.WgsMetricsCollector
  • Constructor Details

    • WgsMetricsWithNonZeroCoverageCollector

      public WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
  • Method Details

    • addToMetricsFile

      public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
      Description copied from class: AbstractWgsMetricsCollector
      Adds collected metrics and depth histogram to file
      Overrides:
      addToMetricsFile in class AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
      Parameters:
      file - MetricsFile for result of collector's work
      dupeFilter - counting filter for duplicate reads
      adapterFilter - counting filter for adapter reads
      mapqFilter - counting filter for mapping quality
      pairFilter - counting filter for reads without a mapped mate pair
    • getDepthHistogram

      protected htsjdk.samtools.util.Histogram<Integer> getDepthHistogram()
    • areHistogramsEmpty

      public boolean areHistogramsEmpty()