Package picard.analysis.directed
Class RnaSeqMetricsCollector
- java.lang.Object
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- picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>
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- picard.metrics.SAMRecordMultiLevelCollector<RnaSeqMetrics,Integer>
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- picard.analysis.directed.RnaSeqMetricsCollector
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public class RnaSeqMetricsCollector extends SAMRecordMultiLevelCollector<RnaSeqMetrics,Integer>
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Nested Class Summary
Nested Classes Modifier and Type Class Description protected class
RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
static class
RnaSeqMetricsCollector.StrandSpecificity
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Field Summary
Fields Modifier and Type Field Description protected Long
ribosomalInitialValue
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Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
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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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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)
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Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector
makeArg
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Methods inherited from class picard.metrics.MultiLevelCollector
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
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Field Detail
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ribosomalInitialValue
protected final Long ribosomalInitialValue
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Constructor Detail
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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)
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Method Detail
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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 classMultiLevelCollector<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 collectorlibrary
- If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collectorreadGroup
- 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
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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)
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