Class/Object

org.bdgenomics.adam.cli

TransformAlignments

Related Docs: object TransformAlignments | package cli

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class TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging

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

  1. new TransformAlignments(args: TransformAlignmentsArgs)

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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. def apply(ds: AlignmentRecordDataset): AlignmentRecordDataset

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  5. val args: TransformAlignmentsArgs

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    Attributes
    protected
    Definition Classes
    TransformAlignments → BDGSparkCommand

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. val companion: TransformAlignments.type

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    Definition Classes
    TransformAlignments → BDGCommand

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  11. def debug(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  13. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  16. def error(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  17. def finalize(): Unit

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

  18. def forceNonParquet(): Boolean

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

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    Definition Classes
    AnyRef → Any

  20. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  23. def info(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    BDGSparkCommand

  25. def isDebugEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  26. def isErrorEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  27. def isInfoEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  28. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  29. def isNonParquet(inputPath: String): Boolean

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  30. def isTraceEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  31. def isWarnEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  32. def logger: Logger

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    Attributes
    protected
    Definition Classes
    Logging

  33. def loggerName: String

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  35. final def notify(): Unit

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    Definition Classes
    AnyRef

  36. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    BDGSparkCommand

  38. def run(sc: SparkContext): Unit

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    Definition Classes
    TransformAlignments → BDGSparkCommand

  39. def run(): Unit

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    Definition Classes
    BDGSparkCommand → Runnable

  40. val stringency: ValidationStringency

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

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    Definition Classes
    AnyRef

  42. def toString(): String

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    Definition Classes
    AnyRef → Any

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  45. def trace(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  46. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  51. def warn(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging

Inherited from BDGSparkCommand[TransformAlignmentsArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped