Class/Object

com.github.heuermh.adam.commands

CountAlignmentsPerRead

Related Docs: object CountAlignmentsPerRead | package commands

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class CountAlignmentsPerRead extends BDGSparkCommand[CountAlignmentsPerReadArgs] with Logging

Count alignments per read ADAM command.

Linear Supertypes
BDGSparkCommand[CountAlignmentsPerReadArgs], Logging, BDGCommand, Runnable, AnyRef, Any
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Inherited
  1. CountAlignmentsPerRead
  2. BDGSparkCommand
  3. Logging
  4. BDGCommand
  5. Runnable
  6. AnyRef
  7. Any
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Visibility
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Instance Constructors

  1. new CountAlignmentsPerRead(args: CountAlignmentsPerReadArgs)

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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. val args: CountAlignmentsPerReadArgs

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    Attributes
    protected
    Definition Classes
    CountAlignmentsPerRead → BDGSparkCommand

  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  6. def clone(): AnyRef

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

  7. val companion: CountAlignmentsPerRead.type

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    Definition Classes
    CountAlignmentsPerRead → BDGCommand

  8. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
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    Logging

  9. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    protected
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    Logging

  10. def debug(msg: ⇒ Any): Unit

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    protected
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    Logging

  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 error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  14. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  15. def error(msg: ⇒ Any): Unit

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    Logging

  16. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  18. def hashCode(): Int

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    AnyRef → Any

  19. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
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    Logging

  20. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  21. def info(msg: ⇒ Any): Unit

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    protected
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    Logging

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

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    Definition Classes
    BDGSparkCommand

  23. def isDebugEnabled: Boolean

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    Attributes
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    Logging

  24. def isErrorEnabled: Boolean

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    Logging

  25. def isInfoEnabled: Boolean

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    Logging

  26. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  27. def isTraceEnabled: Boolean

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    protected
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    Logging

  28. def isWarnEnabled: Boolean

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    Logging

  29. def logger: Logger

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    Logging

  30. def loggerName: String

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    protected
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    Logging

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

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    Definition Classes
    AnyRef

  32. final def notify(): Unit

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    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    BDGSparkCommand

  35. def run(sc: SparkContext): Unit

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    Definition Classes
    CountAlignmentsPerRead → BDGSparkCommand

  36. def run(): Unit

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    Definition Classes
    BDGSparkCommand → Runnable

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

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    Definition Classes
    AnyRef

  38. def toString(): String

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    Definition Classes
    AnyRef → Any

  39. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
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    Logging

  40. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    protected
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    Logging

  41. def trace(msg: ⇒ Any): Unit

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    Attributes
    protected
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    Logging

  42. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  45. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  46. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    protected
    Definition Classes
    Logging

  47. def warn(msg: ⇒ Any): Unit

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    Attributes
    protected
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    Logging

Inherited from BDGSparkCommand[CountAlignmentsPerReadArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped