Package picard.analysis

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

    • Constructor Detail

      • 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 Detail

      • 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<CollectWgsMetrics.WgsMetrics,​Integer> file,
                             boolean includeBQHistogram,
                             CountingFilter dupeFilter,
                             CountingFilter mapqFilter,
                             CountingPairedFilter pairFilter)
        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
        mapqFilter - counting filter for mapping quality
        pairFilter - counting filter for reads without a mapped mate pair