org.bdgenomics.adam.cli

FindReads

class FindReads extends ADAMSparkCommand[FindReadsArgs] with Serializable

Linear Supertypes
Serializable, Serializable, ADAMSparkCommand[FindReadsArgs], Logging, SparkCommand, ADAMCommand, Runnable, AnyRef, Any
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Inherited
  1. FindReads
  2. Serializable
  3. Serializable
  4. ADAMSparkCommand
  5. Logging
  6. SparkCommand
  7. ADAMCommand
  8. Runnable
  9. AnyRef
  10. Any
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  1. Public
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Instance Constructors

  1. new FindReads(args: FindReadsArgs)

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. val args: FindReadsArgs

    Attributes
    protected
    Definition Classes
    FindReads → ADAMSparkCommand

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

  9. val companion: ADAMCommandCompanion

    Definition Classes
    FindReads → ADAMCommand

  10. def createSparkContext(args: SparkArgs, metricsListener: Option[ADAMMetricsListener]): SparkContext

    Definition Classes
    SparkCommand

  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. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  17. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  18. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  30. final def notify(): Unit

    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  32. 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

  33. def printMetrics(totalTime: Long, metricsListener: Option[ADAMMetricsListener]): Unit

    Definition Classes
    ADAMSparkCommand

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

    Definition Classes
    FindReads → ADAMSparkCommand

  35. def run(): Unit

    Definition Classes
    ADAMSparkCommand → Runnable

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

    Definition Classes
    AnyRef

  37. def toString(): String

    Definition Classes
    AnyRef → Any

  38. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from ADAMSparkCommand[FindReadsArgs]

Inherited from Logging

Inherited from SparkCommand

Inherited from ADAMCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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