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
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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 unknownlong
long
long
Fields 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addDuplicateReadToMetrics
(htsjdk.samtools.SAMRecord rec) Adds duplicated read to the metricsvoid
addReadToLibraryMetrics
(htsjdk.samtools.SAMRecord rec) Adds a read to the metricsvoid
Fills 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, main
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
Methods 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:DuplicationMetrics
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.- Overrides:
calculateDerivedFields
in classDuplicationMetrics
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addDuplicateReadToMetrics
public void addDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec) Description copied from class:DuplicationMetrics
Adds duplicated read to the metrics- Overrides:
addDuplicateReadToMetrics
in classDuplicationMetrics
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addReadToLibraryMetrics
public void addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec) Description copied from class:DuplicationMetrics
Adds a read to the metrics- Overrides:
addReadToLibraryMetrics
in classDuplicationMetrics
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