ADAMVariantContext

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: ADAMVariant, genotypes: Iterable[ADAMGenotype], annotation: Option[ADAMDatabaseVariantAnnotation] = None): ADAMVariantContext

   Constructs an ADAMVariantContext from an ADAMVariant and Seq[ADAMGenotype] and ADAMDatabaseVariantAnnotation

   Constructs an ADAMVariantContext from an ADAMVariant and Seq[ADAMGenotype] and ADAMDatabaseVariantAnnotation

   v

   ADAMVariant which is used to construct the ReferencePosition

   genotypes

   Seq[ADAMGenotype]

   annotation

   Option[ADAMDatabaseVariantAnnotation]

   returns

   ADAMVariantContext corresponding to the ADAMVariant

7. def apply(v: ADAMVariant): ADAMVariantContext

   Constructs an ADAMVariantContext from an ADAMVariant

   Constructs an ADAMVariantContext from an ADAMVariant

   v

   ADAMVariant which is used to construct the ReferencePosition

   returns

   ADAMVariantContext corresponding to the ADAMVariant

8. def apply(kv: (ReferencePosition, ADAMVariant, Iterable[ADAMGenotype], Option[ADAMDatabaseVariantAnnotation])): ADAMVariantContext

   Constructs an ADAMVariantContext from locus data.

   Constructs an ADAMVariantContext 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

   ADAMVariantContext corresponding to the data above.

9. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

10. def buildFromGenotypes(genotypes: Seq[ADAMGenotype]): ADAMVariantContext

    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.

11. def clone(): AnyRef

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

13. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

14. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

16. def hashCode(): Int

    Definition Classes

    AnyRef → Any

17. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

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

    Definition Classes

    AnyRef

19. final def notify(): Unit

    Definition Classes

    AnyRef

20. final def notifyAll(): Unit

    Definition Classes

    AnyRef

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

    Definition Classes

    AnyRef

22. def toString(): String

    Definition Classes

    AnyRef → Any

23. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )