Class InsertSizeMetricsCollector


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

      • InsertSizeMetricsCollector

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

      • 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>