Class

org.bdgenomics.cannoli

BcftoolsCall

Related Doc: package cannoli

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class BcftoolsCall extends CannoliFn[VariantContextDataset, VariantContextDataset]

Bcftools call wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

Linear Supertypes
CannoliFn[VariantContextDataset, VariantContextDataset], Logging, (VariantContextDataset) ⇒ VariantContextDataset, AnyRef, Any
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Inherited
  1. BcftoolsCall
  2. CannoliFn
  3. Logging
  4. Function1
  5. AnyRef
  6. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new BcftoolsCall(args: BcftoolsCallArgs, stringency: ValidationStringency = ValidationStringency.LENIENT, sc: SparkContext)

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    args

    Bcftools call function arguments.

    stringency

    Validation stringency. Defaults to ValidationStringency.LENIENT.

    sc

    Spark context.

Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    AnyRef → Any

  4. def absolute(pathName: String): String

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    Definition Classes
    CannoliFn

  5. def andThen[A](g: (VariantContextDataset) ⇒ A): (VariantContextDataset) ⇒ A

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    Definition Classes
    Function1
    Annotations
    @unspecialized()

  6. def apply(variants: VariantContextDataset): VariantContextDataset

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    Definition Classes
    BcftoolsCall → Function1

  7. val args: BcftoolsCallArgs

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    Bcftools call function arguments.

  8. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  9. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  10. def compose[A](g: (A) ⇒ VariantContextDataset): (A) ⇒ VariantContextDataset

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    Definition Classes
    Function1
    Annotations
    @unspecialized()

  11. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  12. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  13. def debug(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  16. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  17. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  18. def error(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  19. def files(pathName: String, filter: PathFilter): Seq[String]

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    Definition Classes
    CannoliFn

  20. def files(pathName: String): Seq[String]

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    Definition Classes
    CannoliFn

  21. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

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    Definition Classes
    AnyRef → Any

  23. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  24. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  25. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  26. def info(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  27. def isDebugEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  28. def isErrorEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  29. def isInfoEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  30. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  31. def isTraceEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  32. def isWarnEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  33. def logger: Logger

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    Attributes
    protected
    Definition Classes
    Logging

  34. def loggerName: String

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  36. final def notify(): Unit

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    Definition Classes
    AnyRef

  37. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  38. def root(pathName: String): String

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    Definition Classes
    CannoliFn

  39. val sc: SparkContext

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    Spark context.

    Spark context.

    Definition Classes
    CannoliFn

  40. val stringency: ValidationStringency

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    Validation stringency.

    Validation stringency. Defaults to ValidationStringency.LENIENT.

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

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    Definition Classes
    AnyRef

  42. def toString(): String

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    Definition Classes
    Function1 → AnyRef → Any

  43. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  44. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  45. def trace(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  46. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  49. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  50. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  51. def warn(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

Inherited from CannoliFn[VariantContextDataset, VariantContextDataset]

Inherited from Logging

Inherited from (VariantContextDataset) ⇒ VariantContextDataset

Inherited from AnyRef

Inherited from Any

Ungrouped