Class

org.biodatageeks.sequila.datasources.VCF

VCFRelation

Related Doc: package VCF

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class VCFRelation extends BaseRelation with PrunedScan with Serializable with Logging

Linear Supertypes
Logging, Serializable, Serializable, PrunedScan, BaseRelation, AnyRef, Any
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Inherited
  1. VCFRelation
  2. Logging
  3. Serializable
  4. Serializable
  5. PrunedScan
  6. BaseRelation
  7. AnyRef
  8. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new VCFRelation(path: String, normalization_mode: Option[String] = None, ref_genome_path: Option[String] = None)(sqlContext: SQLContext)

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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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def buildScan(requiredColumns: Array[String]): RDD[Row]

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    Definition Classes
    VCFRelation → PrunedScan

  6. val cleanContigUDF: UserDefinedFunction

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  7. def clone(): AnyRef

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

  8. lazy val df: DataFrame

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  9. lazy val dfNormalized: DataFrame

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

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    Definition Classes
    AnyRef

  11. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  12. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  14. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  15. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  16. def initializeLogIfNecessary(isInterpreter: Boolean): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  17. lazy val inputDf: DataFrame

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  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. def needConversion: Boolean

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    Definition Classes
    BaseRelation

  34. final def notify(): Unit

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    Definition Classes
    AnyRef

  35. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  36. def schema: StructType

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    Definition Classes
    VCFRelation → BaseRelation

  37. def sizeInBytes: Long

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    Definition Classes
    BaseRelation

  38. val spark: SparkSession

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  39. val sqlContext: SQLContext

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    Definition Classes
    VCFRelation → BaseRelation

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

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    Definition Classes
    AnyRef

  41. def toString(): String

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    Definition Classes
    AnyRef → Any

  42. def unhandledFilters(filters: Array[Filter]): Array[Filter]

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    Definition Classes
    BaseRelation

  43. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from PrunedScan

Inherited from BaseRelation

Inherited from AnyRef

Inherited from Any

Ungrouped