Package picard.sam
Class FlowBasedDuplicationMetrics
- java.lang.Object
-
- htsjdk.samtools.metrics.MetricBase
-
- picard.analysis.MergeableMetricBase
-
- picard.sam.DuplicationMetrics
-
- picard.sam.FlowBasedDuplicationMetrics
-
public class FlowBasedDuplicationMetrics extends DuplicationMetrics
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
-
-
Field Summary
Fields Modifier and Type Field Description Double
UNPAIRED_DUP_RATE_WITH_TLEN
The fraction of duplicated reads out of all reads with exact fragment length knownDouble
UNPAIRED_DUP_RATE_WITHOUT_TLEN
The fraction of duplicated reads out of all reads with exact fragment length unknownlong
UNPAIRED_DUPS_WITH_TLEN
long
UNPAIRED_DUPS_WITHOUT_TLEN
long
UNPAIRED_WITH_TLEN
-
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
-
-
Constructor Summary
Constructors Constructor Description FlowBasedDuplicationMetrics()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec)
Adds duplicated read to the metricsvoid
addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec)
Adds a read to the metricsvoid
calculateDerivedFields()
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
-
-
-
-
Field Detail
-
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
public Double UNPAIRED_DUP_RATE_WITHOUT_TLEN
The fraction of duplicated reads out of all reads with exact fragment length unknown
-
UNPAIRED_DUP_RATE_WITH_TLEN
public Double UNPAIRED_DUP_RATE_WITH_TLEN
The fraction of duplicated reads out of all reads with exact fragment length known
-
-
Method Detail
-
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
-
addDuplicateReadToMetrics
public void addDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec)
Description copied from class:DuplicationMetrics
Adds duplicated read to the metrics- Overrides:
addDuplicateReadToMetrics
in classDuplicationMetrics
-
addReadToLibraryMetrics
public void addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec)
Description copied from class:DuplicationMetrics
Adds a read to the metrics- Overrides:
addReadToLibraryMetrics
in classDuplicationMetrics
-
-