public class RnaSeqMetricsCollector extends SAMRecordMultiLevelCollector<RnaSeqMetrics,Integer>
Modifier and Type | Class and Description |
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static class |
RnaSeqMetricsCollector.StrandSpecificity |
UNKNOWN
Constructor and Description |
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RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
Long ribosomalBasesInitialValue,
OverlapDetector<Gene> geneOverlapDetector,
OverlapDetector<Interval> ribosomalSequenceOverlapDetector,
HashSet<Integer> ignoredSequenceIndices,
int minimumLength,
RnaSeqMetricsCollector.StrandSpecificity strandSpecificity,
double rrnaFragmentPercentage,
boolean collectCoverageStatistics) |
Modifier and Type | Method and Description |
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protected PerUnitMetricCollector<RnaSeqMetrics,Integer,SAMRecord> |
makeChildCollector(String sample,
String library,
String readGroup)
Construct a PerUnitMetricCollector with the given arguments.
|
static HashSet<Integer> |
makeIgnoredSequenceIndicesSet(SAMFileHeader header,
Set<String> ignoredSequence) |
static OverlapDetector<Interval> |
makeOverlapDetector(File samFile,
SAMFileHeader header,
File ribosomalIntervalsFile) |
makeArg
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
public RnaSeqMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, Long ribosomalBasesInitialValue, OverlapDetector<Gene> geneOverlapDetector, OverlapDetector<Interval> ribosomalSequenceOverlapDetector, HashSet<Integer> ignoredSequenceIndices, int minimumLength, RnaSeqMetricsCollector.StrandSpecificity strandSpecificity, double rrnaFragmentPercentage, boolean collectCoverageStatistics)
protected PerUnitMetricCollector<RnaSeqMetrics,Integer,SAMRecord> makeChildCollector(String sample, String library, String readGroup)
MultiLevelCollector
makeChildCollector
in class MultiLevelCollector<RnaSeqMetrics,Integer,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 OverlapDetector<Interval> makeOverlapDetector(File samFile, SAMFileHeader header, File ribosomalIntervalsFile)
public static HashSet<Integer> makeIgnoredSequenceIndicesSet(SAMFileHeader header, Set<String> ignoredSequence)