VariantContext

Value Members

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

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

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3. final def ##(): Int

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

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

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6. def apply(v: Variant, genotypes: Iterable[Genotype], annotation: Option[DatabaseVariantAnnotation] = 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[DatabaseVariantAnnotation]

   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[DatabaseVariantAnnotation])): 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[DatabaseVariantAnnotation]): 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

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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

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

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14. def equals(arg0: Any): Boolean

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15. def finalize(): Unit

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

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17. def hashCode(): Int

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18. final def isInstanceOf[T0]: Boolean

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19. def mergeAnnotations(leftRecord: DatabaseVariantAnnotation, rightRecord: DatabaseVariantAnnotation): DatabaseVariantAnnotation

    Greedily merges two annotation records by filling empty fields.

    Greedily merges two annotation records by filling empty fields.

    Merges two records by taking the union of all fields. If a field is populated in both records, it's value will be taken from the left record.

    leftRecord

    First record to merge. If fields are seen in both records, the value in this record will win.

    rightRecord

    Second record to merge. Used to populate missing fields from the left record.

    returns

    Returns the union of these two annotations.

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

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21. final def notify(): Unit

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22. final def notifyAll(): Unit

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

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24. def toString(): String

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25. final def wait(): Unit

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

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

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