class VariantContextConverter extends Serializable with Logging
This class converts VCF data to and from ADAM. This translation occurs at the abstraction level of the htsjdk VariantContext which represents VCF data, and at the ADAMVariantContext level, which aggregates ADAM variant/genotype/annotation data together.
If a genotype annotation has a corresponding set of fields in the VCF standard, a conversion to/from the htsjdk VariantContext should be implemented in this class.
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- new VariantContextConverter(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency, setNestedAnnotationInGenotype: Boolean)
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def
convert(vc: VariantContext): Option[VariantContext]
Convert an ADAM variant context into a htsjdk variant context.
Convert an ADAM variant context into a htsjdk variant context.
- vc
ADAM variant context to convert.
- returns
The specified ADAM variant context converted into a htsjdk variant context.
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def
convert(vc: VariantContext): Seq[VariantContext]
Converts a htsjdk variant context into one or more ADAM variant context(s).
Converts a htsjdk variant context into one or more ADAM variant context(s).
- vc
htsjdk variant context to convert.
- returns
The specified htsjdk variant context converted into one or more ADAM variant context(s)
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