Field Detail

• metrics

  protected final RnaSeqMetrics metrics

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)

• 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.