Package picard.analysis.directed
Class RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- java.lang.Object
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- picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
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- 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>
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Field Summary
Fields Modifier and Type Field Description protected RnaSeqMetrics
metrics
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Constructor Summary
Constructors Modifier Constructor Description PerUnitRnaSeqMetricsCollector(String sample, String library, String readGroup, Long ribosomalBasesInitialValue)
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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
acceptRecord(htsjdk.samtools.SAMRecord rec)
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)void
addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<RnaSeqMetrics,Integer> file)
Any metrics collected will be added to the metric file provided.void
finish()
When all records have been collected, compute any final values needed to finish constructing metrics/Histogramprotected 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.protected int
getNumAlignedBases(htsjdk.samtools.SAMRecord rec)
Map<Gene.Transcript,int[]>
pickTranscripts(Map<Gene.Transcript,int[]> transcriptCoverage)
Picks the set of transcripts on which the coverage metrics are to be calculated.
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Field Detail
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metrics
protected final RnaSeqMetrics metrics
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Constructor Detail
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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.
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Method Detail
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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 interfacePerUnitMetricCollector<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
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getNumAlignedBases
protected int getNumAlignedBases(htsjdk.samtools.SAMRecord rec)
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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 interfacePerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>
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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 interfacePerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>
- Parameters:
file
- MetricsFile to which all metrics created by this collector should be added
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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.
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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.
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