org.bdgenomics.adam.cli

TransformArgs

class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. TransformArgs
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. SaveArgs
  5. ParquetRDDArgs
  6. Args4jBase
  7. AnyRef
  8. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new TransformArgs()

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any
  3. final def ##(): Int

    Definition Classes
    AnyRef → Any
  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any
  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  7. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs
  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. var coalesce: Int

  10. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs
  11. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs
  12. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase
  13. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  15. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. var forceLoadBam: Boolean

  17. var forceLoadFastq: Boolean

  18. var forceLoadIFastq: Boolean

  19. var forceLoadParquet: Boolean

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

    Definition Classes
    AnyRef → Any
  21. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  22. var inputPath: String

  23. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  24. var knownIndelsFile: String

  25. var knownSnpsFile: String

  26. var locallyRealign: Boolean

  27. var lodThreshold: Double

  28. var logLevel: String

    Definition Classes
    ParquetArgs
  29. var markDuplicates: Boolean

  30. var maxConsensusNumber: Int

  31. var maxIndelSize: Int

  32. var maxTargetSize: Int

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

    Definition Classes
    AnyRef
  34. final def notify(): Unit

    Definition Classes
    AnyRef
  35. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  36. var observationsPath: String

  37. var outputPath: String

    Definition Classes
    TransformArgs → SaveArgs
  38. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs
  39. var printMetrics: Boolean

    Definition Classes
    Args4jBase
  40. var recalibrateBaseQualities: Boolean

  41. var repartition: Int

  42. var sortFastqOutput: Boolean

    Definition Classes
    TransformArgs → ADAMSaveAnyArgs
  43. var sortReads: Boolean

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

    Definition Classes
    AnyRef
  45. def toString(): String

    Definition Classes
    AnyRef → Any
  46. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  47. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  48. final def wait(arg0: Long): Unit

    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

Ungrouped