class VariantContextToInternalRowConverter extends GlowLogging with HasStringency with Serializable
Converts an HTSJDK variant context into a SparkSQL row with the provided schema.
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new
VariantContextToInternalRowConverter(header: VCFHeader, schema: StructType, stringency: ValidationStringency, writeSampleIds: Boolean = true)
- header
The VCF header for this dataset
- schema
The actual for the emitted rows
- stringency
How strictly to validate input variant contexts. If strict, incorrect rows will result in an exception. If lenient, we'll do a best effort to parse the row and log warnings. If silent, best effort and continue.
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- def convertRow(vc: VariantContext, priorRow: InternalRow, isSplit: Boolean): InternalRow
- def convertRow(vc: VariantContext, isSplit: Boolean): InternalRow
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stringency: ValidationStringency
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