implicit class CannoliVariantContextDataset extends AnyRef
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Instance Constructors
- new CannoliVariantContextDataset(vcs: VariantContextDataset)
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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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.
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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.
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final
def
asInstanceOf[T0]: T0
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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.
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def
clone(): AnyRef
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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final
def
ne(arg0: AnyRef): Boolean
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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.
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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.
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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