org.hammerlab.guacamole.jointcaller.annotation

MultiSampleAnnotations

case class MultiSampleAnnotations(insufficientNormal: Option[InsufficientNormal]) extends Product with Serializable

Annotation for multiple samples at a single allele and a single site.

We use "annotations" to compute extra statistics about a call that can get put in the VCF. This enables us to break variant calling into a cheaper operation where we compute likelihoods to see if a call can be made, and then later compute all the annotations to gather extra info and decide if it fails any filters.

Annotations can be filters by implementing the optional isFiltered method. If that returns true, the call is considered filtered.

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Instance Constructors

  1. new MultiSampleAnnotations(insufficientNormal: Option[InsufficientNormal])

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. def addInfoToVCF(builder: VariantContextBuilder): Unit

  7. def annotationsFailingFilters: Seq[Annotation]

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. val insufficientNormal: Option[InsufficientNormal]

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    AnyRef

  19. def toSeq: Seq[Annotation]

  20. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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