org.bdgenomics.adam.cli

Transform

class Transform extends ADAMSparkCommand[TransformArgs] with Logging

Linear Supertypes
ADAMSparkCommand[TransformArgs], Logging, ADAMCommand, Runnable, AnyRef, Any
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Inherited
  1. Transform
  2. ADAMSparkCommand
  3. Logging
  4. ADAMCommand
  5. Runnable
  6. AnyRef
  7. Any
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Instance Constructors

  1. new Transform(args: TransformArgs)

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. def apply(rdd: RDD[AlignmentRecord]): RDD[AlignmentRecord]

  7. val args: TransformArgs

    Attributes
    protected
    Definition Classes
    Transform → ADAMSparkCommand

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def clone(): AnyRef

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

  10. val companion: Transform.type

    Definition Classes
    Transform → ADAMCommand

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

    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  13. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  15. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  16. def initializeMetrics(sc: SparkContext): Option[MetricsListener]

    Definition Classes
    ADAMSparkCommand

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  18. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  19. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

  20. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  21. def logDebug(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  22. def logError(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  23. def logError(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  24. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  25. def logInfo(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  26. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

  27. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  28. def logTrace(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  29. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  30. def logWarning(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  32. final def notify(): Unit

    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  34. def printMetrics(totalTime: Long, metricsListener: Option[MetricsListener]): Unit

    Definition Classes
    ADAMSparkCommand

  35. def run(sc: SparkContext, job: Job): Unit

    Definition Classes
    Transform → ADAMSparkCommand

  36. def run(): Unit

    Definition Classes
    ADAMSparkCommand → Runnable

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

    Definition Classes
    AnyRef

  38. def toString(): String

    Definition Classes
    AnyRef → Any

  39. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ADAMSparkCommand[TransformArgs]

Inherited from Logging

Inherited from ADAMCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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