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.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    long
    DUPLICATE_SETS_IGNORING_UMI
    Number of duplicate sets found before taking UMIs into account
    long
    DUPLICATE_SETS_WITH_UMI
    Number of duplicate sets found after taking UMIs into account
    double
    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 derived
    String
    LIBRARY
    Library that was used to generate UMI data.
    double
    MEAN_UMI_LENGTH
    Number of bases in each UMI
    long
    OBSERVED_BASE_ERRORS
    Number of errors inferred by comparing the observed and inferred UMIs
    double
    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 observed
    double
    PCT_UMI_WITH_N
    The percentage of reads that contain an UMI that contains at least one N
    double
    UMI_BASE_QUALITIES
    Estimation of Phred scaled quality scores for UMIs

  • 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)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addUmiObservation(String observedUmi, String inferredUmi)
    Add an observation of a UMI to the metrics
    void
    addUmiObservationN()
    Add an observation of a UMI containing at least one N to the metrics
    void
    calculateDerivedFields()
     

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • LIBRARY

      public String LIBRARY
      Library that was used to generate UMI data.

    • MEAN_UMI_LENGTH

      public double MEAN_UMI_LENGTH
      Number of bases in each UMI

    • OBSERVED_UNIQUE_UMIS

      public long OBSERVED_UNIQUE_UMIS
      Number of different UMI sequences observed

    • INFERRED_UNIQUE_UMIS

      public long INFERRED_UNIQUE_UMIS
      Number of different inferred UMI sequences derived

    • OBSERVED_BASE_ERRORS

      public long OBSERVED_BASE_ERRORS
      Number of errors inferred by comparing the observed and inferred UMIs

    • DUPLICATE_SETS_IGNORING_UMI

      public long DUPLICATE_SETS_IGNORING_UMI
      Number of duplicate sets found before taking UMIs into account

    • DUPLICATE_SETS_WITH_UMI

      public long DUPLICATE_SETS_WITH_UMI
      Number of duplicate sets found after taking UMIs into account

    • 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.

    • 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.

    • UMI_BASE_QUALITIES

      public double UMI_BASE_QUALITIES
      Estimation of Phred scaled quality scores for UMIs

    • PCT_UMI_WITH_N

      public double PCT_UMI_WITH_N
      The percentage of reads that contain an UMI that contains at least one N

  • Constructor Details

    • UmiMetrics

      public UmiMetrics()

    • UmiMetrics

      public UmiMetrics(String library)

    • 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)

  • Method Details

    • calculateDerivedFields

      public void calculateDerivedFields()

    • addUmiObservation

      public void addUmiObservation(String observedUmi, String inferredUmi)
      Add an observation of a UMI to the metrics
      Parameters:
      observedUmi - String containing the observed UMI
      inferredUmi - String containing the UMI inferred after error correcting the observed UMI

    • addUmiObservationN

      public void addUmiObservationN()
      Add an observation of a UMI containing at least one N to the metrics