Cannoli_2.12: Core 1.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package cannoli
  Definition Classes
    bdgenomics
-  object Cannoli

  Implicits on Cannoli function source data sets.

  Implicits on Cannoli function source data sets.

  Definition Classes
    cannoli
- CannoliAlignmentDataset
- CannoliFeatureDataset
- CannoliFragmentDataset
- CannoliReadDataset
- CannoliSequenceDataset
- CannoliVariantContextDataset

c

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
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
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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9.  final def eq(arg0: AnyRef): Boolean
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10.  def equals(arg0: Any): Boolean
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11.  def finalize(): Unit
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12.  final def getClass(): Class[_]
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      @native()
13.  def hashCode(): Int
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      @native()
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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      @throws( ... )
23.  final def wait(arg0: Long, arg1: Int): Unit
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      @throws( ... )
24.  final def wait(arg0: Long): Unit
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### Inherited from AnyRef

### Inherited from Any

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