Class TargetMetricsCollector.PerUnitTargetMetricCollector

    • Constructor Summary

      Constructors 
      Constructor Description
      PerUnitTargetMetricCollector​(String probeSetName, Set<htsjdk.samtools.util.Interval> coverageTargets, String sample, String library, String readGroup, long probeTerritory, long targetTerritory, long genomeSize, Map<htsjdk.samtools.util.Interval,​Double> intervalToGc, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean includeIndels)
      Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
    • Constructor Detail

      • PerUnitTargetMetricCollector

        public PerUnitTargetMetricCollector​(String probeSetName,
                                            Set<htsjdk.samtools.util.Interval> coverageTargets,
                                            String sample,
                                            String library,
                                            String readGroup,
                                            long probeTerritory,
                                            long targetTerritory,
                                            long genomeSize,
                                            Map<htsjdk.samtools.util.Interval,​Double> intervalToGc,
                                            int minimumMappingQuality,
                                            int minimumBaseQuality,
                                            boolean clipOverlappingReads,
                                            boolean includeIndels)
        Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
    • Method Detail

      • setPerTargetOutput

        public void setPerTargetOutput​(File perTargetOutput)
        Sets the (optional) File to write per-target coverage information to. If null (the default), no file is produced.
      • setPerBaseOutput

        public void setPerBaseOutput​(File perBaseOutput)
        Sets the (optional) File to write per-base coverage information to. If null (the default), no file is produced.
      • setBaitSetName

        public void setBaitSetName​(String name)
        Sets the name of the bait set explicitly instead of inferring it from the bait file.
      • getCoverageByTarget

        public Map<htsjdk.samtools.util.Interval,​TargetMetricsCollector.Coverage> getCoverageByTarget()
        Returns the accumulated coverage per target. Note that while the returned Map is immutable, it is possible that the underlying Map will continue to be mutated if the map is retrieved prior to additional calls to acceptRecord(SAMRecord).
      • acceptRecord

        public void acceptRecord​(htsjdk.samtools.SAMRecord record)
        Adds information about an individual SAMRecord to the statistics.
        Specified by:
        acceptRecord in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,​Integer,​htsjdk.samtools.SAMRecord>
        Parameters:
        record - Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class