Package picard.analysis.directed

Class RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector

java.lang.Object
picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
All Implemented Interfaces:
PerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>
Enclosing class:
RnaSeqMetricsCollector
protected class RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector extends Object implements PerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>

  • Field Details

  • Constructor Details

    • 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 Details

    • 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)

    • 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<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>

    • addMetricsToFile

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

    • 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.