Package picard.sam.markduplicates
Class UmiMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.sam.markduplicates.UmiMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class UmiMetrics
extends htsjdk.samtools.metrics.MetricBase
Metrics that are calculated during the process of marking duplicates
within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
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Field Summary
Modifier and TypeFieldDescriptionlong
Number of duplicate sets found before taking UMIs into accountlong
Number of duplicate sets found after taking UMIs into accountdouble
Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.long
Number of different inferred UMI sequences derivedLibrary that was used to generate UMI data.double
Number of bases in each UMIlong
Number of errors inferred by comparing the observed and inferred UMIsdouble
Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.long
Number of different UMI sequences observeddouble
The percentage of reads that contain an UMI that contains at least one Ndouble
Estimation of Phred scaled quality scores for UMIs -
Constructor Summary
ConstructorDescriptionUmiMetrics
(String library) UmiMetrics
(String library, double length, int observedUniqueUmis, int inferredUniqueUmis, int observedBaseErrors, int duplicateSetsWithoutUmi, int duplicateSetsWithUmi, double effectiveLengthOfInferredUmis, double effectiveLengthOfObservedUmis, double estimatedBaseQualityOfUmis, double percentUmiWithN) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addUmiObservation
(String observedUmi, String inferredUmi) Add an observation of a UMI to the metricsvoid
Add an observation of a UMI containing at least one N to the metricsvoid
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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LIBRARY
Library that was used to generate UMI data. -
MEAN_UMI_LENGTH
public double MEAN_UMI_LENGTHNumber of bases in each UMI -
OBSERVED_UNIQUE_UMIS
public long OBSERVED_UNIQUE_UMISNumber of different UMI sequences observed -
INFERRED_UNIQUE_UMIS
public long INFERRED_UNIQUE_UMISNumber of different inferred UMI sequences derived -
OBSERVED_BASE_ERRORS
public long OBSERVED_BASE_ERRORSNumber of errors inferred by comparing the observed and inferred UMIs -
DUPLICATE_SETS_IGNORING_UMI
public long DUPLICATE_SETS_IGNORING_UMINumber of duplicate sets found before taking UMIs into account -
DUPLICATE_SETS_WITH_UMI
public long DUPLICATE_SETS_WITH_UMINumber of duplicate sets found after taking UMIs into account -
OBSERVED_UMI_ENTROPY
public double OBSERVED_UMI_ENTROPYEntropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly. -
INFERRED_UMI_ENTROPY
public double INFERRED_UMI_ENTROPYEntropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly. -
UMI_BASE_QUALITIES
public double UMI_BASE_QUALITIESEstimation of Phred scaled quality scores for UMIs -
PCT_UMI_WITH_N
public double PCT_UMI_WITH_NThe percentage of reads that contain an UMI that contains at least one N
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Constructor Details
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UmiMetrics
public UmiMetrics() -
UmiMetrics
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UmiMetrics
public UmiMetrics(String library, double length, int observedUniqueUmis, int inferredUniqueUmis, int observedBaseErrors, int duplicateSetsWithoutUmi, int duplicateSetsWithUmi, double effectiveLengthOfInferredUmis, double effectiveLengthOfObservedUmis, double estimatedBaseQualityOfUmis, double percentUmiWithN)
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Method Details
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calculateDerivedFields
public void calculateDerivedFields() -
addUmiObservation
Add an observation of a UMI to the metrics- Parameters:
observedUmi
- String containing the observed UMIinferredUmi
- String containing the UMI inferred after error correcting the observed UMI
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addUmiObservationN
public void addUmiObservationN()Add an observation of a UMI containing at least one N to the metrics
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