Class InsertSizeMetricsCollector

java.lang.Object
picard.metrics.MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
picard.analysis.directed.InsertSizeMetricsCollector

public class InsertSizeMetricsCollector extends MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
Collects InsertSizeMetrics on the specified accumulationLevels using
  • Constructor Details

    • InsertSizeMetricsCollector

      public InsertSizeMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, double minimumPct, Integer histogramWidth, Integer minHistogramWidth, double deviations, boolean includeDuplicates)
  • Method Details

    • makeArg

      protected picard.analysis.directed.InsertSizeCollectorArgs makeArg(htsjdk.samtools.SAMRecord samRecord, htsjdk.samtools.reference.ReferenceSequence refSeq)
      Specified by:
      makeArg in class MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
    • makeChildCollector

      protected PerUnitMetricCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs> makeChildCollector(String sample, String library, String readGroup)
      Make an InsertSizeCollector with the given arguments
      Specified by:
      makeChildCollector in class MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>
      Parameters:
      sample - If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collector
      library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector
      readGroup - If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector
      Returns:
      A PerUnitMetricCollector parameterized by the given arguments
    • acceptRecord

      public void acceptRecord(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequence refSeq)
      Description copied from class: MultiLevelCollector
      Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
      Overrides:
      acceptRecord in class MultiLevelCollector<InsertSizeMetrics,Integer,picard.analysis.directed.InsertSizeCollectorArgs>