Package picard.analysis.directed

Class RnaSeqMetricsCollector

java.lang.Object

picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>

picard.metrics.SAMRecordMultiLevelCollector<RnaSeqMetrics,Integer>

picard.analysis.directed.RnaSeqMetricsCollector

public class RnaSeqMetricsCollector
extends SAMRecordMultiLevelCollector<RnaSeqMetrics,Integer>

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
static enum	RnaSeqMetricsCollector.StrandSpecificity

Field Summary

Fields

Modifier and Type	Field	Description
static final int	defaultEndBiasBases
protected final Long	ribosomalInitialValue

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor	Description
RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, Long ribosomalBasesInitialValue, htsjdk.samtools.util.OverlapDetector<Gene> geneOverlapDetector, htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> ribosomalSequenceOverlapDetector, HashSet<Integer> ignoredSequenceIndices, int minimumLength, RnaSeqMetricsCollector.StrandSpecificity strandSpecificity, double rrnaFragmentPercentage, boolean collectCoverageStatistics)
RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, Long ribosomalBasesInitialValue, htsjdk.samtools.util.OverlapDetector<Gene> geneOverlapDetector, htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> ribosomalSequenceOverlapDetector, HashSet<Integer> ignoredSequenceIndices, int minimumLength, RnaSeqMetricsCollector.StrandSpecificity strandSpecificity, double rrnaFragmentPercentage, boolean collectCoverageStatistics, int endBiasBases)

Method Summary

Modifier and Type	Method	Description
protected PerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>	makeChildCollector(String sample, String library, String readGroup)	Construct a PerUnitMetricCollector with the given arguments.
static HashSet<Integer>	makeIgnoredSequenceIndicesSet(htsjdk.samtools.SAMFileHeader header, Set<String> ignoredSequence)
static htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval>	makeOverlapDetector(File samFile, htsjdk.samtools.SAMFileHeader header, File ribosomalIntervalsFile, htsjdk.samtools.util.Log log)

Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector

makeArg

Methods inherited from class picard.metrics.MultiLevelCollector

acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup

Methods inherited from class java.lang.Object

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

Field Details

ribosomalInitialValue

protected final Long ribosomalInitialValue

defaultEndBiasBases

public static final int defaultEndBiasBases

See Also:

• Constant Field Values

Constructor Details

RnaSeqMetricsCollector

public RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
 List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
 Long ribosomalBasesInitialValue,
 htsjdk.samtools.util.OverlapDetector<Gene> geneOverlapDetector,
 htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> ribosomalSequenceOverlapDetector,
 HashSet<Integer> ignoredSequenceIndices,
 int minimumLength,
 RnaSeqMetricsCollector.StrandSpecificity strandSpecificity,
 double rrnaFragmentPercentage,
 boolean collectCoverageStatistics,
 int endBiasBases)

RnaSeqMetricsCollector

public RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
 List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
 Long ribosomalBasesInitialValue,
 htsjdk.samtools.util.OverlapDetector<Gene> geneOverlapDetector,
 htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> ribosomalSequenceOverlapDetector,
 HashSet<Integer> ignoredSequenceIndices,
 int minimumLength,
 RnaSeqMetricsCollector.StrandSpecificity strandSpecificity,
 double rrnaFragmentPercentage,
 boolean collectCoverageStatistics)

Method Details

makeChildCollector

protected PerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord> makeChildCollector(String sample,
 String library,
 String readGroup)

Description copied from class: MultiLevelCollector

Construct a PerUnitMetricCollector with the given arguments.

Specified by:

makeChildCollector in class MultiLevelCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>

Parameters:

sample - If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collector

library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector

readGroup - If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector

Returns:

A PerUnitMetricCollector parameterized by the given arguments

makeOverlapDetector

public static htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> makeOverlapDetector(File samFile,
 htsjdk.samtools.SAMFileHeader header,
 File ribosomalIntervalsFile,
 htsjdk.samtools.util.Log log)

makeIgnoredSequenceIndicesSet

public static HashSet<Integer> makeIgnoredSequenceIndicesSet(htsjdk.samtools.SAMFileHeader header,
 Set<String> ignoredSequence)