Class UmiMetrics


  • 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 Detail

      • 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 Detail

      • 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 Detail

      • 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