org.bdgenomics.adam.models

# VariantContext

#### object VariantContext

Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object. If you're looking for the latter, see org.bdgenomics.adam.rdd.variation.VariationContext

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1. #### final def !=(arg0: Any): Boolean

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2. #### final def ##(): Int

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3. #### final def ==(arg0: Any): Boolean

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4. #### 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

5. #### 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

6. #### 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.

7. #### final def asInstanceOf[T0]: T0

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8. #### 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.

9. #### def clone(): AnyRef

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