Class IndependentReplicateMetric


  • public class IndependentReplicateMetric
    extends MergeableMetricBase
    A class to store information relevant for biological rate estimation
    • Field Detail

      • nThreeAllelesSites

        public Integer nThreeAllelesSites
      • nTotalReads

        public Integer nTotalReads
      • nDuplicateSets

        public Integer nDuplicateSets
      • nExactlyTriple

        public Integer nExactlyTriple
      • nExactlyDouble

        public Integer nExactlyDouble
      • nReadsInBigSets

        public Integer nReadsInBigSets
      • nDifferentAllelesBiDups

        public Integer nDifferentAllelesBiDups
      • nReferenceAllelesBiDups

        public Integer nReferenceAllelesBiDups
      • nAlternateAllelesBiDups

        public Integer nAlternateAllelesBiDups
      • nDifferentAllelesTriDups

        public Integer nDifferentAllelesTriDups
      • nMismatchingAllelesBiDups

        public Integer nMismatchingAllelesBiDups
      • nReferenceAllelesTriDups

        public Integer nReferenceAllelesTriDups
      • nAlternateAllelesTriDups

        public Integer nAlternateAllelesTriDups
      • nMismatchingAllelesTriDups

        public Integer nMismatchingAllelesTriDups
      • nReferenceReads

        public Integer nReferenceReads
      • nAlternateReads

        public Integer nAlternateReads
      • nMismatchingUMIsInDiffBiDups

        public Integer nMismatchingUMIsInDiffBiDups
      • nMatchingUMIsInDiffBiDups

        public Integer nMatchingUMIsInDiffBiDups
      • nMismatchingUMIsInSameBiDups

        public Integer nMismatchingUMIsInSameBiDups
      • nMatchingUMIsInSameBiDups

        public Integer nMatchingUMIsInSameBiDups
      • nMismatchingUMIsInCoOrientedBiDups

        public Integer nMismatchingUMIsInCoOrientedBiDups
      • nMismatchingUMIsInContraOrientedBiDups

        public Integer nMismatchingUMIsInContraOrientedBiDups
      • nBadBarcodes

        public Integer nBadBarcodes
      • nGoodBarcodes

        public Integer nGoodBarcodes
      • biSiteHeterogeneityRate

        public Double biSiteHeterogeneityRate
      • triSiteHeterogeneityRate

        public Double triSiteHeterogeneityRate
      • biSiteHomogeneityRate

        public Double biSiteHomogeneityRate
      • triSiteHomogeneityRate

        public Double triSiteHomogeneityRate
      • independentReplicationRateFromBiDups

        public Double independentReplicationRateFromBiDups
      • independentReplicationRateFromTriDups

        public Double independentReplicationRateFromTriDups
      • pSameUmiInIndependentBiDup

        public Double pSameUmiInIndependentBiDup
      • pSameAlleleWhenMismatchingUmi

        public Double pSameAlleleWhenMismatchingUmi
      • independentReplicationRateFromUmi

        public Double independentReplicationRateFromUmi
      • replicationRateFromReplicateSets

        public Double replicationRateFromReplicateSets
    • Constructor Detail

      • IndependentReplicateMetric

        public IndependentReplicateMetric()
    • Method Detail

      • calculateDerivedFields

        public void calculateDerivedFields()
        Description copied from class: MergeableMetricBase
        Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
        Overrides:
        calculateDerivedFields in class MergeableMetricBase