Class/Object

org.bdgenomics.adam.rich

RichGenotype

Related Docs: object RichGenotype | package rich

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class RichGenotype extends AnyRef

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Instance Constructors

  1. new RichGenotype(genotype: Genotype)

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Value Members

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

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  2. final def ##(): Int

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

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  4. final def asInstanceOf[T0]: T0

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  5. def clone(): AnyRef

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

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  7. def equals(arg0: Any): Boolean

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  8. def finalize(): Unit

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  9. val genotype: Genotype

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

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  11. def getType: GenotypeType

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  12. def hashCode(): Int

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  13. def isCalled: Boolean

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    True if the genotype does not contain any alleles that are not called.

    True if the genotype does not contain any alleles that are not called. e.g. './.' or '0/.' in VCF

  14. def isHet: Boolean

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    True if we're het (observed alleles differ); if the ploidy is less than 2 or if any alleles are no-calls, this method will return false.

  15. def isHom: Boolean

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    True if all observed alleles are the same (regardless of whether they are ref or alt); if any alleles are no-calls, this method will return false.

  16. def isHomAlt: Boolean

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    True if all observed alleles are alt; if any alleles are no-calls, this method will return false.

  17. def isHomRef: Boolean

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    True if all observed alleles are ref; if any alleles are no-calls, this method will return false.

  18. final def isInstanceOf[T0]: Boolean

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  19. def isNoCall: Boolean

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    True if this genotype is not actually a genotype but a "no call" (e.g.

    True if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF). Also true for partial no call genotypes (e.g. '0/.' in VCF)

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

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  21. final def notify(): Unit

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  22. final def notifyAll(): Unit

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  23. def ploidy: Int

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

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  25. def toString(): String

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  26. final def wait(): Unit

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

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

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