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
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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: AlignmentDataset): AlignmentDataset

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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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    protected
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    Logging

  11. def debug(msg: ⇒ Any): Unit

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    protected
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    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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  16. def error(msg: ⇒ Any): Unit

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  17. def finalize(): Unit

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    Attributes
    protected[java.lang]
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    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
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    Logging

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

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  23. def info(msg: ⇒ Any): Unit

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  24. def isDebugEnabled: Boolean

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    Logging

  25. def isErrorEnabled: Boolean

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    Logging

  26. def isInfoEnabled: Boolean

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    Logging

  27. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  28. def isNonParquet(inputPath: String): Boolean

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  29. def isTraceEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  30. def isWarnEnabled: Boolean

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    Attributes
    protected
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    Logging

  31. def logger: Logger

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    Logging

  32. def loggerName: String

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    Attributes
    protected
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    Logging

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

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    Definition Classes
    AnyRef

  34. final def notify(): Unit

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    Definition Classes
    AnyRef

  35. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  36. def run(sc: SparkContext): Unit

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    Definition Classes
    TransformAlignments → BDGSparkCommand

  37. def run(): Unit

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    Definition Classes
    BDGSparkCommand → Runnable

  38. val stringency: ValidationStringency

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

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    Definition Classes
    AnyRef

  40. def toString(): String

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    Definition Classes
    AnyRef → Any

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    protected
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    Logging

  43. def trace(msg: ⇒ Any): Unit

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    Attributes
    protected
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    Logging

  44. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Logging

  49. def warn(msg: ⇒ Any): Unit

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    Attributes
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    Logging

Inherited from BDGSparkCommand[TransformAlignmentsArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped