Class RnaSeqMetricsCollector

    • Field Detail

      • ribosomalInitialValue

        protected final Long ribosomalInitialValue
    • Constructor Detail

      • RnaSeqMetricsCollector

        public RnaSeqMetricsCollector​(Set<MetricAccumulationLevel> accumulationLevels,
                                      List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                                      Long ribosomalBasesInitialValue,
                                      htsjdk.samtools.util.OverlapDetector<Gene> geneOverlapDetector,
                                      htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> ribosomalSequenceOverlapDetector,
                                      HashSet<Integer> ignoredSequenceIndices,
                                      int minimumLength,
                                      RnaSeqMetricsCollector.StrandSpecificity strandSpecificity,
                                      double rrnaFragmentPercentage,
                                      boolean collectCoverageStatistics)
    • Method Detail

      • makeChildCollector

        protected PerUnitMetricCollector<RnaSeqMetrics,​Integer,​htsjdk.samtools.SAMRecord> makeChildCollector​(String sample,
                                                                                                                         String library,
                                                                                                                         String readGroup)
        Description copied from class: MultiLevelCollector
        Construct a PerUnitMetricCollector with the given arguments.
        Specified by:
        makeChildCollector in class MultiLevelCollector<RnaSeqMetrics,​Integer,​htsjdk.samtools.SAMRecord>
        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
      • makeOverlapDetector

        public static htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> makeOverlapDetector​(File samFile,
                                                                                                              htsjdk.samtools.SAMFileHeader header,
                                                                                                              File ribosomalIntervalsFile,
                                                                                                              htsjdk.samtools.util.Log log)
      • makeIgnoredSequenceIndicesSet

        public static HashSet<Integer> makeIgnoredSequenceIndicesSet​(htsjdk.samtools.SAMFileHeader header,
                                                                     Set<String> ignoredSequence)