public class RnaSeqMetricsCollector extends SAMRecordMultiLevelCollector<RnaSeqMetrics,Integer>
Modifier and Type | Class | Description |
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protected class |
RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector |
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static class |
RnaSeqMetricsCollector.StrandSpecificity |
Modifier and Type | Field | Description |
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protected Long |
ribosomalInitialValue |
UNKNOWN
Constructor | Description |
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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) |
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) |
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
makeArg
protected final Long ribosomalInitialValue
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)
protected PerUnitMetricCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord> makeChildCollector(String sample, String library, String readGroup)
MultiLevelCollector
makeChildCollector
in class MultiLevelCollector<RnaSeqMetrics,Integer,htsjdk.samtools.SAMRecord>
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 collectorpublic static htsjdk.samtools.util.OverlapDetector<htsjdk.samtools.util.Interval> makeOverlapDetector(File samFile, htsjdk.samtools.SAMFileHeader header, File ribosomalIntervalsFile)