Package picard.sam.markduplicates

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