org.bdgenomics.adam.cli

ADAMSparkCommand

trait ADAMSparkCommand[A <: Args4jBase with SparkArgs] extends ADAMCommand with SparkCommand with Logging

Linear Supertypes
Logging, SparkCommand, ADAMCommand, Runnable, AnyRef, Any
Known Subclasses
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Inherited
  1. ADAMSparkCommand
  2. Logging
  3. SparkCommand
  4. ADAMCommand
  5. Runnable
  6. AnyRef
  7. Any
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Abstract Value Members

  1. abstract val args: A

    Attributes
    protected
  2. abstract val companion: ADAMCommandCompanion

    Definition Classes
    ADAMCommand
  3. abstract def run(sc: SparkContext, job: Job): Unit

Concrete 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. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  7. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def createSparkContext(args: SparkArgs, metricsListener: Option[ADAMMetricsListener]): SparkContext

    Definition Classes
    SparkCommand
  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. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  16. def log: Logger

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

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

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

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

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

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

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

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

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

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

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

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

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

    Definition Classes
    AnyRef
  30. def parseEnvVariables(envVariables: ArrayList[String]): Array[(String, String)]

    Commandline format is -spark_env foo=1 -spark_env bar=2

    Commandline format is -spark_env foo=1 -spark_env bar=2

    envVariables

    The variables found on the commandline

    returns

    Definition Classes
    SparkCommand
  31. def printMetrics(totalTime: Long, metricsListener: Option[ADAMMetricsListener]): Unit

  32. def run(): Unit

    Definition Classes
    ADAMSparkCommand → Runnable
  33. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  34. def toString(): String

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

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Logging

Inherited from SparkCommand

Inherited from ADAMCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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