Class

org.bdgenomics.adam.cli

TransformFragmentsArgs

Related Doc: package cli

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class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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Inherited
  1. TransformFragmentsArgs
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. SaveArgs
  5. ParquetRDDArgs
  6. Args4jBase
  7. AnyRef
  8. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new TransformFragmentsArgs()

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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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. var asSingleFile: Boolean

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    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  6. var binQualityScores: String

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  7. var blockSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  8. def clone(): AnyRef

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

  9. var compressionCodec: CompressionCodecName

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  10. var deferMerging: Boolean

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    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  11. var disableDictionaryEncoding: Boolean

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  12. var disableFastConcat: Boolean

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    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  13. var doPrintUsage: Boolean

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    Definition Classes
    Args4jBase

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

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    Definition Classes
    AnyRef

  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  16. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    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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    Definition Classes
    AnyRef → Any

  19. var inputPath: String

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  20. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  21. var loadAsAlignments: Boolean

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  22. var logLevel: String

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    Definition Classes
    ParquetArgs

  23. var markDuplicates: Boolean

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  24. var maxReadLength: Int

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

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    Definition Classes
    AnyRef

  26. final def notify(): Unit

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    Definition Classes
    AnyRef

  27. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  28. var outputPath: String

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    Definition Classes
    TransformFragmentsArgs → SaveArgs

  29. var pageSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  30. var saveAsAlignments: Boolean

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  31. var sortByReadName: Boolean

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  32. var sortByReferencePosition: Boolean

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  33. var sortByReferencePositionAndIndex: Boolean

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  34. var sortFastqOutput: Boolean

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    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  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 ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

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