Interface WgsMetricsProcessor

All Known Implementing Classes:
WgsMetricsProcessorImpl

public interface WgsMetricsProcessor
Interface for processing data and generate result for CollectWgsMetrics
  • Method Details

    • processFile

      void processFile()
      Method processes the input data and accumulates result data
    • addToMetricsFile

      void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
      Adds result metric's data to input file
      Parameters:
      file - MetricsFile for result of collector's work
      includeBQHistogram - include base quality histogram
      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