Field Detail

• nSites

  public Integer nSites

  The count of sites used.

• nThreeAllelesSites

  public Integer nThreeAllelesSites

  The count of sites in which a third allele was found.

• nTotalReads

  public Integer nTotalReads

  The total number of reads over the het sites.

• nDuplicateSets

  public Integer nDuplicateSets

  The number of duplicate sets examined.

• nExactlyTriple

  public Integer nExactlyTriple

  The number of sets of size exactly 3 found.

• nExactlyDouble

  public Integer nExactlyDouble

  The number of sets of size exactly 2 found.

• nReadsInBigSets

  public Integer nReadsInBigSets

  The number of reads in duplicate of sizes greater than 3.

• nDifferentAllelesBiDups

  public Integer nDifferentAllelesBiDups

  The number of doubletons where the two reads had different bases in the locus.

• nReferenceAllelesBiDups

  public Integer nReferenceAllelesBiDups

  The number of doubletons where the two reads matched the reference.

• nAlternateAllelesBiDups

  public Integer nAlternateAllelesBiDups

  The number of doubletons where the two reads matched the alternate.

• nDifferentAllelesTriDups

  public Integer nDifferentAllelesTriDups

  The number of tripletons where at least one of the reads didn't match either allele of the het site.

• nMismatchingAllelesBiDups

  public Integer nMismatchingAllelesBiDups

  The number of tripletons where the two reads had different bases in the locus.

• nReferenceAllelesTriDups

  public Integer nReferenceAllelesTriDups

  The number of tripletons where the two reads matched the reference.

• nAlternateAllelesTriDups

  public Integer nAlternateAllelesTriDups

  The number of tripletons where the two reads matched the alternate.

• nMismatchingAllelesTriDups

  public Integer nMismatchingAllelesTriDups

  The number of tripletons where at least one of the reads didn't match either allele of the het site.

• nReferenceReads

  public Integer nReferenceReads

  The number of reference alleles in the reads.

• nAlternateReads

  public Integer nAlternateReads

  The number of alternate alleles in the reads.

• nMismatchingUMIsInDiffBiDups

  public Integer nMismatchingUMIsInDiffBiDups

  The number of UMIs that are different within Bi-sets that come from different alleles.

• nMatchingUMIsInDiffBiDups

  public Integer nMatchingUMIsInDiffBiDups

  The number of UMIs that are match within Bi-sets that come from different alleles.

• nMismatchingUMIsInSameBiDups

  public Integer nMismatchingUMIsInSameBiDups

  The number of UMIs that are different within Bi-sets that come from the same alleles.

• nMatchingUMIsInSameBiDups

  public Integer nMatchingUMIsInSameBiDups

  The number of UMIs that are match within Bi-sets that come from the same alleles.

• nMismatchingUMIsInCoOrientedBiDups

  public Integer nMismatchingUMIsInCoOrientedBiDups

  The number of bi-sets with mismatching UMIs and same orientation.

• nMismatchingUMIsInContraOrientedBiDups

  public Integer nMismatchingUMIsInContraOrientedBiDups

  The number of bi-sets with mismatching UMIs and opposite orientation.

• nBadBarcodes

  public Integer nBadBarcodes

  The number of sets where the UMIs had poor quality bases and were not used for any comparisons.

• nGoodBarcodes

  public Integer nGoodBarcodes

  the number of sets where the UMIs had good quality bases and were used for any comparisons.

• biSiteHeterogeneityRate

  public Double biSiteHeterogeneityRate

  the rate of heterogeneity within doubleton sets.

• triSiteHeterogeneityRate

  public Double triSiteHeterogeneityRate

  the rate of heterogeneity within tripleton sets

• biSiteHomogeneityRate

  public Double biSiteHomogeneityRate

  the rate of homogeneity within doubleton sets.

• triSiteHomogeneityRate

  public Double triSiteHomogeneityRate

  the rate of homogeneity within tripleton sets.

• independentReplicationRateFromBiDups

  public Double independentReplicationRateFromBiDups

• independentReplicationRateFromTriDups

  public Double independentReplicationRateFromTriDups

  The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.

• pSameUmiInIndependentBiDup

  public Double pSameUmiInIndependentBiDup

  When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance). So we expect this to be near 1.

• pSameAlleleWhenMismatchingUmi

  public Double pSameAlleleWhenMismatchingUmi

  When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5

• independentReplicationRateFromUmi

  public Double independentReplicationRateFromUmi

  Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets. This is only a good estimate if the assumptions hold, for example if pSameUmiInIndependentBiDup is near 1.

• replicationRateFromReplicateSets

  public Double replicationRateFromReplicateSets

  An estimate of the duplication rate that is based on the duplicate sets we observed.

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