org.hammerlab.guacamole.jointcaller.evidence

TumorDNASingleSampleSingleAlleleEvidence

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.

allele

allele under consideration

allelicDepths

Map from sequenced bases -> number of reads supporting that allele

logLikelihoods

Map from allelic mixtures to log10 likelihoods

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Serializable, Serializable, Product, Equals, SingleSampleSingleAlleleEvidence, AnyRef, Any
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  1. TumorDNASingleSampleSingleAlleleEvidence
  2. Serializable
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  4. Product
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  6. SingleSampleSingleAlleleEvidence
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Instance Constructors

  1. new TumorDNASingleSampleSingleAlleleEvidence(allele: AlleleAtLocus, allelicDepths: Map[String, Int], logLikelihoods: Map[AlleleMixture, Double], annotations: Option[SingleSampleAnnotations] = scala.None)

    allele

    allele under consideration

    allelicDepths

    Map from sequenced bases -> number of reads supporting that allele

    logLikelihoods

    Map from allelic mixtures to log10 likelihoods

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. val allele: AlleleAtLocus

    allele under consideration

    allele under consideration

    Definition Classes
    TumorDNASingleSampleSingleAlleleEvidence → SingleSampleSingleAlleleEvidence

  7. val allelicDepths: Map[String, Int]

    Map from sequenced bases -> number of reads supporting that allele

  8. val annotations: Option[SingleSampleAnnotations]

    extra information, including filters, we compute about a potential call

    extra information, including filters, we compute about a potential call

    Definition Classes
    TumorDNASingleSampleSingleAlleleEvidence → SingleSampleSingleAlleleEvidence

  9. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  10. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  11. def depth(): Int

    Total depth of all reads contributing an allele.

  12. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  13. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  14. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  16. val logLikelihoods: Map[AlleleMixture, Double]

    Map from allelic mixtures to log10 likelihoods

  17. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  18. final def notify(): Unit

    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  20. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  21. def vaf(): Double

    Fraction of reads supporting this allele (variant allele frequency).

  22. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  23. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  24. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  25. def withAnnotations(newAnnotations: SingleSampleAnnotations): TumorDNASingleSampleSingleAlleleEvidence

    return a new instance including the given annotations

    return a new instance including the given annotations

    Definition Classes
    TumorDNASingleSampleSingleAlleleEvidence → SingleSampleSingleAlleleEvidence

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from SingleSampleSingleAlleleEvidence

Inherited from AnyRef

Inherited from Any

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