class InternalRowToVariantContextConverter extends GlowLogging with HasStringency with Serializable
Converts internal rows with the provided schema into HTSJDK variant context.
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new
InternalRowToVariantContextConverter(rowSchema: StructType, headerLineSet: Set[VCFHeaderLine], stringency: ValidationStringency)
- rowSchema
The schema of the rows that will be converted by this instance. The schema must match the provided rows exactly.
- headerLineSet
VCF header lines used for validation. The header is only used to provide warnings or validation errors if the fields in the data either don't exist in the header or have incompatible types. These warnings/errors can be useful if downstream calculations depend on certain fields being present.
- stringency
How seriously to treat validation errors vs the VCF header.
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- def convert(row: InternalRow): Option[VariantContext]
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provideWarning(warning: String): Unit
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val
stringency: ValidationStringency
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- val vcfHeader: VCFHeader
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