Class

org.bdgenomics.cannoli

BcftoolsMpileup

Related Doc: package cannoli

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class BcftoolsMpileup extends CannoliFn[AlignmentRecordDataset, VariantContextDataset] with Logging

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

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

Instance Constructors

  1. new BcftoolsMpileup(args: BcftoolsMpileupArgs, stringency: ValidationStringency = ValidationStringency.LENIENT, sc: SparkContext)

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    args

    Bcftools mpileup 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): (AlignmentRecordDataset) ⇒ A

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    Definition Classes
    Function1
    Annotations
    @unspecialized()
  6. def apply(alignments: AlignmentRecordDataset): VariantContextDataset

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    Definition Classes
    BcftoolsMpileup → Function1
  7. val args: BcftoolsMpileupArgs

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    Bcftools mpileup 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) ⇒ AlignmentRecordDataset): (A) ⇒ VariantContextDataset

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    Definition Classes
    Function1
    Annotations
    @unspecialized()
  11. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  12. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  13. def files(pathName: String, filter: PathFilter): Seq[String]

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    Definition Classes
    CannoliFn
  14. def files(pathName: String): Seq[String]

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    Definition Classes
    CannoliFn
  15. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  17. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  19. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  20. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  21. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  22. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  23. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  24. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  25. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  26. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  27. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging
  28. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  29. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  30. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  31. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  32. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  33. final def notify(): Unit

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    Definition Classes
    AnyRef
  34. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  35. def root(pathName: String): String

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    Definition Classes
    CannoliFn
  36. val sc: SparkContext

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    Spark context.

    Spark context.

    Definition Classes
    CannoliFn
  37. val stringency: ValidationStringency

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    Validation stringency.

    Validation stringency. Defaults to ValidationStringency.LENIENT.

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

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    Definition Classes
    AnyRef
  39. def toString(): String

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    Definition Classes
    Function1 → AnyRef → Any
  40. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  41. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  42. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Logging

Inherited from CannoliFn[AlignmentRecordDataset, VariantContextDataset]

Inherited from (AlignmentRecordDataset) ⇒ VariantContextDataset

Inherited from AnyRef

Inherited from Any

Ungrouped