picard.analysis.directed

Class RnaSeqMetricsCollector

java.lang.Object

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

picard.metrics.SAMRecordMultiLevelCollector<RnaSeqMetrics,java.lang.Integer>

picard.analysis.directed.RnaSeqMetricsCollector

public class RnaSeqMetricsCollector
extends SAMRecordMultiLevelCollector<RnaSeqMetrics,java.lang.Integer>

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.Long	ribosomalInitialValue

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor and Description

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

Method Summary

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

ribosomalInitialValue

protected final java.lang.Long ribosomalInitialValue

Constructor Detail

RnaSeqMetricsCollector

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

Method Detail

makeChildCollector

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

Description copied from class: MultiLevelCollector

Construct a PerUnitMetricCollector with the given arguments.

Specified by:

makeChildCollector in class MultiLevelCollector<RnaSeqMetrics,java.lang.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(java.io.File samFile,
                                                                                                      htsjdk.samtools.SAMFileHeader header,
                                                                                                      java.io.File ribosomalIntervalsFile,
                                                                                                      htsjdk.samtools.util.Log log)

makeIgnoredSequenceIndicesSet

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