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 Summary

Fields

Modifier and Type	Field	Description
protected final RnaSeqMetrics	metrics

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.

Method Summary

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/Histogram
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.
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

metrics

protected final RnaSeqMetrics metrics

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.