evidence

Type Members

1. case class MultiSampleMultiAlleleEvidence(contigName: ContigName, start: Locus, singleAlleleEvidences: Seq[MultiSampleSingleAlleleEvidence]) extends ReferenceRegion with Product with Serializable

   A grouping of AlleleEvidenceAcrossSamples instances (one for each allele) at the same site.

2. case class MultiSampleSingleAlleleEvidence(parameters: Parameters, allele: AlleleAtLocus, inputs: InputCollection, normalDNAPooledEvidence: NormalDNASingleSampleSingleAlleleEvidence, tumorDNAPooledEvidence: TumorDNASingleSampleSingleAlleleEvidence, sampleEvidences: PerSample[SingleSampleSingleAlleleEvidence], annotations: Option[MultiSampleAnnotations]) extends Product with Serializable

   Summarizes the evidence for a single allele across any number of samples.

3. case class NormalDNASingleSampleSingleAlleleEvidence(allele: AlleleAtLocus, allelicDepths: Map[String, Int], logLikelihoods: Map[(String, String), Double], annotations: Option[SingleSampleAnnotations] = scala.None) extends SingleSampleSingleAlleleEvidence with Product with Serializable

   Summary of evidence for a particular germline allele in a single normal DNA sample.

4. trait SingleSampleSingleAlleleEvidence extends AnyRef

   Summary of evidence for an allele at a site in a single sample.

5. case class TumorDNASingleSampleSingleAlleleEvidence(allele: AlleleAtLocus, allelicDepths: Map[String, Int], logLikelihoods: Map[AlleleMixture, Double], annotations: Option[SingleSampleAnnotations] = scala.None) extends SingleSampleSingleAlleleEvidence with Product with Serializable

   Summary of evidence for a particular somatic allele in a single tumor DNA sample.

6. case class TumorRNASingleSampleSingleAlleleEvidence(allele: AlleleAtLocus, allelicDepths: Map[String, Int], logLikelihoods: Map[AlleleMixture, Double], annotations: Option[SingleSampleAnnotations] = scala.None) extends SingleSampleSingleAlleleEvidence with Product with Serializable

   Summary of evidence for a particular somatic allele in a single tumor RNA sample.