VariantContext

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 apply(v: Variant, genotypes: Iterable[Genotype], annotation: Option[VariantAnnotation] = None): VariantContext

   Constructs an VariantContext from an Variant and Seq[Genotype] and DatabaseVariantAnnotation

   Constructs an VariantContext from an Variant and Seq[Genotype] and DatabaseVariantAnnotation

   v

   Variant which is used to construct the ReferencePosition

   genotypes

   Seq[Genotype]

   annotation

   Option[VariantAnnotation]

   returns

   VariantContext corresponding to the Variant

7. def apply(v: Variant): VariantContext

   Constructs an VariantContext from an Variant

   Constructs an VariantContext from an Variant

   v

   Variant which is used to construct the ReferencePosition

   returns

   VariantContext corresponding to the Variant

8. def apply(kv: (ReferencePosition, Variant, Iterable[Genotype], Option[VariantAnnotation])): VariantContext

   Constructs an VariantContext from locus data.

   Constructs an VariantContext from locus data. Used in merger process.

   kv

   Nested tuple containing (locus on reference, (variants at site, genotypes at site, optional domain annotation at site))

   returns

   VariantContext corresponding to the data above.

9. def apply(v: VariantContext, optAnn: Option[VariantAnnotation]): VariantContext

   Produces a new variant context by merging with an optional annotation.

   Produces a new variant context by merging with an optional annotation.

   If the existing context doesn't have an annotation, pick the new annotation, if present. If both exist, then merge.

   v

   An existing VariantContext to annotate.

   optAnn

   An optional annotation to add.

   returns

   A new VariantContext, where an annotation has been added/merged.

10. final def asInstanceOf[T0]: T0

    Definition Classes

    Any

11. def buildFromGenotypes(genotypes: Seq[Genotype]): VariantContext

    Builds a variant context off of a set of genotypes.

    Builds a variant context off of a set of genotypes. Builds variants from the genotypes.

    genotypes

    List of genotypes to build variant context from.

    returns

    A variant context corresponding to the variants and genotypes at this site.

    Note

    Genotypes must be at the same position.

12. def clone(): AnyRef

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

14. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

15. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes

    AnyRef → Any

17. def hashCode(): Int

    Definition Classes

    AnyRef → Any

18. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

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

    Definition Classes

    AnyRef

20. final def notify(): Unit

    Definition Classes

    AnyRef

21. final def notifyAll(): Unit

    Definition Classes

    AnyRef

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

    Definition Classes

    AnyRef

23. def toString(): String

    Definition Classes

    AnyRef → Any

24. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )