Interface WgsMetricsProcessor

  • All Known Implementing Classes:
    WgsMetricsProcessorImpl

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

      • processFile

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

        void addToMetricsFile​(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,​Integer> file,
                              boolean includeBQHistogram,
                              CountingFilter dupeFilter,
                              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
        mapqFilter - counting filter for mapping quality
        pairFilter - counting filter for reads without a mapped mate pair