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org.bdgenomics.cannoli.Cannoli

CannoliVariantContextDataset

implicit class CannoliVariantContextDataset extends AnyRef

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Instance Constructors

  1. new CannoliVariantContextDataset(vcs: VariantContextDataset)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
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  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. def annotateWithSnpEff(args: SnpEffArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

    Annotate the variant contexts in this VariantContextDataset with SnpEff via Cannoli.

    Annotate the variant contexts in this VariantContextDataset with SnpEff via Cannoli.

    args

    SnpEff function arguments.

    stringency

    Validation stringency. Defaults to ValidationStringency.LENIENT.

    returns

    VariantContextDataset.

  5. def annotateWithVep(args: VepArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

    Annotate the variant contexts in this VariantContextDataset with Ensembl VEP via Cannoli.

    Annotate the variant contexts in this VariantContextDataset with Ensembl VEP via Cannoli.

    args

    Vep function arguments.

    stringency

    Validation stringency. Defaults to ValidationStringency.LENIENT.

    returns

    VariantContextDataset.

  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. def callWithBcftools(args: BcftoolsCallArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

    Call variant contexts in this VariantContextDataset with bcftools call via Cannoli.

    Call variant contexts in this VariantContextDataset with bcftools call via Cannoli.

    args

    Bcftools call function arguments.

    stringency

    Validation stringency. Defaults to ValidationStringency.LENIENT.

    returns

    VariantContextDataset.

  8. def clone(): AnyRef
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    @throws( ... ) @native()
  9. final def eq(arg0: AnyRef): Boolean
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  10. def equals(arg0: Any): Boolean
    Definition Classes
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  11. def finalize(): Unit
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  12. final def getClass(): Class[_]
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  13. def hashCode(): Int
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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. def normalizeWithBcftools(args: BcftoolsNormArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

    Normalize the variant contexts in this VariantContextDataset with bcftools norm via Cannoli.

    Normalize the variant contexts in this VariantContextDataset with bcftools norm via Cannoli.

    args

    Bcftools norm function arguments.

    stringency

    Validation stringency. Defaults to ValidationStringency.LENIENT.

    returns

    VariantContextDataset.

  17. def normalizeWithVt(args: VtNormalizeArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

    Normalize the variant contexts in this VariantContextDataset with vt normalize via Cannoli.

    Normalize the variant contexts in this VariantContextDataset with vt normalize via Cannoli.

    args

    Vt normalize function arguments.

    stringency

    Validation stringency. Defaults to ValidationStringency.LENIENT.

    returns

    VariantContextDataset.

  18. final def notify(): Unit
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    @native()
  19. final def notifyAll(): Unit
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    @native()
  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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