Class RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector

    • Constructor Detail

      • PerUnitRnaSeqMetricsCollector

        protected PerUnitRnaSeqMetricsCollector​(RnaSeqMetrics metrics,
                                                String sample,
                                                String library,
                                                String readGroup,
                                                Long ribosomalBasesInitialValue)
        Derived classes that need to capture some additional metrics can use this ctor to supply a metrics instance that is a subclass of RnaSeqMetrics.
      • PerUnitRnaSeqMetricsCollector

        public PerUnitRnaSeqMetricsCollector​(String sample,
                                             String library,
                                             String readGroup,
                                             Long ribosomalBasesInitialValue)
    • Method Detail

      • acceptRecord

        public void acceptRecord​(htsjdk.samtools.SAMRecord rec)
        Description copied from interface: PerUnitMetricCollector
        Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
        Specified by:
        acceptRecord in interface PerUnitMetricCollector<RnaSeqMetrics,​Integer,​htsjdk.samtools.SAMRecord>
        Parameters:
        rec - Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class
      • getNumAlignedBases

        protected int getNumAlignedBases​(htsjdk.samtools.SAMRecord rec)
      • getGenesForPickTranscripts

        protected Set<Gene> getGenesForPickTranscripts()
        Derived class may override this method in order to return a different set of genes for picking transcripts for computing coverage, or to cache the value returned by geneOverlapDetector.getAll(), because it can be expensive to compute repeatedly.
      • pickTranscripts

        public Map<Gene.Transcript,​int[]> pickTranscripts​(Map<Gene.Transcript,​int[]> transcriptCoverage)
        Picks the set of transcripts on which the coverage metrics are to be calculated.