Constructs an VariantContext from an Variant and Seq[Genotype] and DatabaseVariantAnnotation
Constructs an VariantContext from an Variant and Seq[Genotype] and DatabaseVariantAnnotation
Variant which is used to construct the ReferencePosition
Seq[Genotype]
Option[DatabaseVariantAnnotation]
VariantContext corresponding to the Variant
Constructs an VariantContext from an Variant
Constructs an VariantContext from an Variant
Variant which is used to construct the ReferencePosition
VariantContext corresponding to the Variant
Constructs an VariantContext from locus data.
Constructs an VariantContext from locus data. Used in merger process.
Nested tuple containing (locus on reference, (variants at site, genotypes at site, optional domain annotation at site))
VariantContext corresponding to the data above.
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.
An existing VariantContext to annotate.
An optional annotation to add.
A new VariantContext, where an annotation has been added/merged.
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.
List of genotypes to build variant context from.
A variant context corresponding to the variants and genotypes at this site.
Genotypes must be at the same position.
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.
First record to merge. If fields are seen in both records, the value in this record will win.
Second record to merge. Used to populate missing fields from the left record.
Returns the union of these two annotations.
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