Package picard.sam.markduplicates
Class UmiMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.sam.markduplicates.UmiMetrics
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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
Fields Modifier and Type Field Description long
DUPLICATE_SETS_IGNORING_UMI
Number of duplicate sets found before taking UMIs into accountlong
DUPLICATE_SETS_WITH_UMI
Number of duplicate sets found after taking UMIs into accountdouble
INFERRED_UMI_ENTROPY
Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.long
INFERRED_UNIQUE_UMIS
Number of different inferred UMI sequences derivedString
LIBRARY
Library that was used to generate UMI data.double
MEAN_UMI_LENGTH
Number of bases in each UMIlong
OBSERVED_BASE_ERRORS
Number of errors inferred by comparing the observed and inferred UMIsdouble
OBSERVED_UMI_ENTROPY
Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.long
OBSERVED_UNIQUE_UMIS
Number of different UMI sequences observeddouble
PCT_UMI_WITH_N
The percentage of reads that contain an UMI that contains at least one Ndouble
UMI_BASE_QUALITIES
Estimation of Phred scaled quality scores for UMIs
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Constructor Summary
Constructors Constructor Description UmiMetrics()
UmiMetrics(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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addUmiObservation(String observedUmi, String inferredUmi)
Add an observation of a UMI to the metricsvoid
addUmiObservationN()
Add an observation of a UMI containing at least one N to the metricsvoid
calculateDerivedFields()
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Field Detail
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LIBRARY
public String LIBRARY
Library that was used to generate UMI data.
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MEAN_UMI_LENGTH
public double MEAN_UMI_LENGTH
Number of bases in each UMI
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OBSERVED_UNIQUE_UMIS
public long OBSERVED_UNIQUE_UMIS
Number of different UMI sequences observed
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INFERRED_UNIQUE_UMIS
public long INFERRED_UNIQUE_UMIS
Number of different inferred UMI sequences derived
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OBSERVED_BASE_ERRORS
public long OBSERVED_BASE_ERRORS
Number of errors inferred by comparing the observed and inferred UMIs
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DUPLICATE_SETS_IGNORING_UMI
public long DUPLICATE_SETS_IGNORING_UMI
Number of duplicate sets found before taking UMIs into account
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DUPLICATE_SETS_WITH_UMI
public long DUPLICATE_SETS_WITH_UMI
Number of duplicate sets found after taking UMIs into account
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OBSERVED_UMI_ENTROPY
public double OBSERVED_UMI_ENTROPY
Entropy (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.
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INFERRED_UMI_ENTROPY
public double INFERRED_UMI_ENTROPY
Entropy (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.
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UMI_BASE_QUALITIES
public double UMI_BASE_QUALITIES
Estimation of Phred scaled quality scores for UMIs
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PCT_UMI_WITH_N
public double PCT_UMI_WITH_N
The percentage of reads that contain an UMI that contains at least one N
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Constructor Detail
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UmiMetrics
public UmiMetrics()
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UmiMetrics
public UmiMetrics(String library)
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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 Detail
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calculateDerivedFields
public void calculateDerivedFields()
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addUmiObservation
public void addUmiObservation(String observedUmi, String inferredUmi)
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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