org.bdgenomics.adam.converters

VariantAnnotationConverter

object VariantAnnotationConverter extends Serializable

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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

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

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

    Definition Classes
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  6. val CLINVAR_KEYS: List[AttrKey]

  7. val COSMIC_KEYS: List[AttrKey]

  8. val DBNSFP_KEYS: List[AttrKey]

  9. val FORMAT_KEYS: Seq[AttrKey]

  10. val INFO_KEYS: Seq[AttrKey]

  11. val OMIM_KEYS: List[AttrKey]

  12. lazy val VCF2DatabaseAnnotations: Map[String, (Int, (AnyRef) ⇒ AnyRef)]

  13. lazy val VCF2GenotypeAnnotations: Map[String, (Int, (AnyRef) ⇒ AnyRef)]

  14. lazy val VCF2VariantCallingAnnotations: Map[String, (Int, (AnyRef) ⇒ AnyRef)]

  15. final def asInstanceOf[T0]: T0

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  16. def clone(): AnyRef

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

  17. def convert(g: Genotype, genotype: Genotype): Genotype

  18. def convert(vc: VariantContext, call: VariantCallingAnnotations): VariantCallingAnnotations

  19. def convert(vc: VariantContext, annotation: DatabaseVariantAnnotation): DatabaseVariantAnnotation

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

    Definition Classes
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  21. def equals(arg0: Any): Boolean

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  22. def finalize(): Unit

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

  23. lazy val formatHeaderLines: Seq[VCFCompoundHeaderLine]

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

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  25. def hashCode(): Int

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  26. lazy val infoHeaderLines: Seq[VCFCompoundHeaderLine]

  27. final def isInstanceOf[T0]: Boolean

    Definition Classes
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  28. def mergeAnnotations(leftRecord: DatabaseVariantAnnotation, rightRecord: DatabaseVariantAnnotation): DatabaseVariantAnnotation

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

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  30. final def notify(): Unit

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  31. final def notifyAll(): Unit

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

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  33. def toString(): String

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  34. final def wait(): Unit

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    @throws( ... )

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

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

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