Class TargetMetricsCollector.PerUnitTargetMetricCollector

java.lang.Object
picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
All Implemented Interfaces:
PerUnitMetricCollector<METRIC_TYPE,Integer,htsjdk.samtools.SAMRecord>
Enclosing class:
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>

public class TargetMetricsCollector.PerUnitTargetMetricCollector extends Object implements PerUnitMetricCollector<METRIC_TYPE,Integer,htsjdk.samtools.SAMRecord>
Collect the Target Metrics for one unit of "accumulation" (i.e. for one sample, or for one library ...)
  • 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.
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    acceptRecord(htsjdk.samtools.SAMRecord record)
    Adds information about an individual SAMRecord to the statistics.
    void
    addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE,Integer> hsMetricsComparableMetricsFile)
    Any metrics collected will be added to the metric file provided.
    void
    When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
    Map<htsjdk.samtools.util.Interval,TargetMetricsCollector.Coverage>
    Returns the accumulated coverage per target.
    void
    Sets the name of the bait set explicitly instead of inferring it from the bait file.
    void
    setPerBaseOutput(File perBaseOutput)
    Sets the (optional) File to write per-base coverage information to.
    void
    setPerTargetOutput(File perTargetOutput)
    Sets the (optional) File to write per-target coverage information to.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • 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 Details

    • 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
    • finish

      public void finish()
      Description copied from interface: PerUnitMetricCollector
      When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
      Specified by:
      finish in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,Integer,htsjdk.samtools.SAMRecord>
    • addMetricsToFile

      public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE,Integer> hsMetricsComparableMetricsFile)
      Description copied from interface: PerUnitMetricCollector
      Any metrics collected will be added to the metric file provided.
      Specified by:
      addMetricsToFile in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,Integer,htsjdk.samtools.SAMRecord>
      Parameters:
      hsMetricsComparableMetricsFile - MetricsFile to which all metrics created by this collector should be added