org.bdgenomics.adam.converters

VariantContextConverter

object VariantContextConverter extends Serializable

Object for converting between htsjdk and ADAM VariantContexts.

Handles Variant, Genotype, Allele, and various genotype annotation conversions. Does not handle Variant annotations. Genotype annotations are annotations in the VCF GT field while Variant annotations are annotations contained in the VCF INFO field.

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  1. final def !=(arg0: AnyRef): Boolean

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  2. final def !=(arg0: Any): Boolean

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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  5. final def ==(arg0: Any): Boolean

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  6. def apply(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency, conf: Configuration): VariantContextConverter

  7. final def asInstanceOf[T0]: T0

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  8. def clone(): AnyRef

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  11. def finalize(): Unit

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  12. final def getClass(): Class[_]

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  14. final def isInstanceOf[T0]: Boolean

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  15. final def ne(arg0: AnyRef): Boolean

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  16. val nestAnnotationInGenotypesProperty: String

    If set to true, this property will ensure that the variant.

    If set to true, this property will ensure that the variant.annotation field in the Genotype record is populated after conversion from an htsjdk VariantContext. By default, this property is false.

  17. final def notify(): Unit

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  18. final def notifyAll(): Unit

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  19. def setNestAnnotationInGenotypesProperty(conf: Configuration, populateNestedAnn: Boolean): Unit

    Sets the value of the nest annotation in genotypes property.

    Sets the value of the nest annotation in genotypes property.

    conf

    Hadoop configuration to set the property in.

    populateNestedAnn

    If true, the nested field is populated.

  20. final def synchronized[T0](arg0: ⇒ T0): T0

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  21. def toString(): String

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  22. final def wait(): Unit

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  24. final def wait(arg0: Long): Unit

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