CannoliVariantContextDataset

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

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   

   Definition Classes

   AnyRef

10. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

11. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    

    Definition Classes

    AnyRef → Any

13. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

14. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

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

    

    Definition Classes

    AnyRef

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

    

    Definition Classes

    AnyRef

19. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

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

    

    Definition Classes

    AnyRef

21. def toString(): String

    

    Definition Classes

    AnyRef → Any

22. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )