Class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>

java.lang.Object
picard.analysis.WgsMetricsProcessorImpl<T>
All Implemented Interfaces:
WgsMetricsProcessor

public class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> extends Object implements WgsMetricsProcessor
Implementation of WgsMetricsProcessor that gets input data from a given iterator and processes it with a help of collector
  • Constructor Details

    • WgsMetricsProcessorImpl

      public WgsMetricsProcessorImpl(htsjdk.samtools.util.AbstractLocusIterator<T,htsjdk.samtools.util.AbstractLocusInfo<T>> iterator, htsjdk.samtools.reference.ReferenceSequenceFileWalker refWalker, AbstractWgsMetricsCollector<T> collector, htsjdk.samtools.util.ProgressLogger progress)
      Parameters:
      iterator - input AbstractLocusIterator
      refWalker - over processed reference file
      collector - input AbstractWgsMetricsCollector
      progress - logger
  • Method Details

    • processFile

      public void processFile()
      Method gets the data from iterator for each locus and processes it with the help of collector.
      Specified by:
      processFile in interface WgsMetricsProcessor
    • addToMetricsFile

      public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
      Description copied from interface: WgsMetricsProcessor
      Adds result metric's data to input file
      Specified by:
      addToMetricsFile in interface WgsMetricsProcessor
      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