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 GATK variant context.
Convert an ADAM variant context into a GATK variant context.
- vc
ADAM variant context to convert.
- returns
The specified ADAM variant context converted into a GATK variant context.
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def
convert(vc: VariantContext): Seq[VariantContext]
Converts a GATK variant context into one or more ADAM variant context(s).
Converts a GATK variant context into one or more ADAM variant context(s).
- vc
GATK variant context to convert.
- returns
The specified GATK variant context converted into one or more ADAM variant context(s)
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