org.bdgenomics.adam.converters

VariantContextConverter

class VariantContextConverter extends Serializable

This class converts VCF data to and from ADAM. This translation occurs at the abstraction level of the GATK VariantContext which represents VCF data, and at the ADAMVariantContext level, which aggregates ADAM variant/genotype/annotation data together.

If an annotation has a corresponding set of fields in the VCF standard, a conversion to/from the GATK VariantContext should be implemented in this class.

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Instance Constructors

  1. new VariantContextConverter(dict: Option[SequenceDictionary] = scala.None)

Value Members

  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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  7. def clone(): AnyRef

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    protected[java.lang]
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    @throws( ... )

  8. def convert(vc: ADAMVariantContext): VariantContext

    Convert an ADAMVariantContext into the equivalent GATK VariantContext

    Convert an ADAMVariantContext into the equivalent GATK VariantContext

    vc
    returns

    GATK VariantContext

  9. def convert(vc: VariantContext, extractExternalAnnotations: Boolean = false): Seq[ADAMVariantContext]

    Converts a single GATK variant into ADAMVariantContext(s).

    Converts a single GATK variant into ADAMVariantContext(s).

    vc

    GATK Variant context to convert.

    returns

    ADAM variant contexts

  10. def convertToAnnotation(vc: VariantContext): ADAMDatabaseVariantAnnotation

  11. final def eq(arg0: AnyRef): Boolean

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  12. def equals(arg0: Any): Boolean

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  13. def finalize(): Unit

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

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  15. def hashCode(): Int

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  16. final def isInstanceOf[T0]: Boolean

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

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  18. final def notify(): Unit

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  19. final def notifyAll(): Unit

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  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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  23. final def wait(arg0: Long, arg1: Int): Unit

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

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