Class/Object

org.bdgenomics.adam.cli

TransformGenotypes

Related Docs: object TransformGenotypes | package cli

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class TransformGenotypes extends BDGSparkCommand[TransformGenotypesArgs]

Convert a file with genotypes into corresponding ADAM format and vice versa.

Linear Supertypes
BDGSparkCommand[TransformGenotypesArgs], Logging, BDGCommand, Runnable, AnyRef, Any
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Inherited
  1. TransformGenotypes
  2. BDGSparkCommand
  3. Logging
  4. BDGCommand
  5. Runnable
  6. AnyRef
  7. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new TransformGenotypes(args: TransformGenotypesArgs)

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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: TransformGenotypesArgs

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    Definition Classes
    TransformGenotypes → 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: TransformGenotypes.type

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    Definition Classes
    TransformGenotypes → BDGCommand

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

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    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  10. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  12. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    BDGSparkCommand

  14. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  15. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  16. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  23. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  29. final def notify(): Unit

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    Definition Classes
    AnyRef

  30. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    BDGSparkCommand

  32. def run(sc: SparkContext): Unit

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    Definition Classes
    TransformGenotypes → BDGSparkCommand

  33. def run(): Unit

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    Definition Classes
    BDGSparkCommand → Runnable

  34. val stringency: ValidationStringency

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

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    Definition Classes
    AnyRef

  36. def toString(): String

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    Definition Classes
    AnyRef → Any

  37. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from BDGSparkCommand[TransformGenotypesArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped