Package picard.sam
Class FlowBasedDuplicationMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.DuplicationMetrics
picard.sam.FlowBasedDuplicationMetrics
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Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue -
Field Summary
FieldsModifier and TypeFieldDescriptionThe fraction of duplicated reads out of all reads with exact fragment length knownThe fraction of duplicated reads out of all reads with exact fragment length unknownlonglonglongFields inherited from class picard.sam.DuplicationMetrics
ESTIMATED_LIBRARY_SIZE, LIBRARY, PERCENT_DUPLICATION, READ_PAIR_DUPLICATES, READ_PAIR_OPTICAL_DUPLICATES, READ_PAIRS_EXAMINED, SECONDARY_OR_SUPPLEMENTARY_RDS, UNMAPPED_READS, UNPAIRED_READ_DUPLICATES, UNPAIRED_READS_EXAMINED -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidaddDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec) Adds duplicated read to the metricsvoidaddReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec) Adds a read to the metricsvoidFills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.Methods inherited from class picard.sam.DuplicationMetrics
calculateDerivedMetrics, calculateRoiHistogram, estimateLibrarySize, estimateRoi, mainMethods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCanMethods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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UNPAIRED_WITH_TLEN
public long UNPAIRED_WITH_TLEN -
UNPAIRED_DUPS_WITHOUT_TLEN
public long UNPAIRED_DUPS_WITHOUT_TLEN -
UNPAIRED_DUPS_WITH_TLEN
public long UNPAIRED_DUPS_WITH_TLEN -
UNPAIRED_DUP_RATE_WITHOUT_TLEN
The fraction of duplicated reads out of all reads with exact fragment length unknown -
UNPAIRED_DUP_RATE_WITH_TLEN
The fraction of duplicated reads out of all reads with exact fragment length known
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Constructor Details
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FlowBasedDuplicationMetrics
public FlowBasedDuplicationMetrics()
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Method Details
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calculateDerivedFields
public void calculateDerivedFields()Description copied from class:DuplicationMetricsFills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.- Overrides:
calculateDerivedFieldsin classDuplicationMetrics
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addDuplicateReadToMetrics
public void addDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec) Description copied from class:DuplicationMetricsAdds duplicated read to the metrics- Overrides:
addDuplicateReadToMetricsin classDuplicationMetrics
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addReadToLibraryMetrics
public void addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec) Description copied from class:DuplicationMetricsAdds a read to the metrics- Overrides:
addReadToLibraryMetricsin classDuplicationMetrics
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