org.bdgenomics.adam.cli

TransformArgs

class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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Inherited
  1. TransformArgs
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. SaveArgs
  5. ParquetRDDArgs
  6. Args4jBase
  7. AnyRef
  8. Any
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  1. Public
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Instance Constructors

  1. new TransformArgs()

Value Members

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

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  5. var asSingleFile: Boolean

    Definition Classes
    TransformArgs → ADAMSaveAnyArgs

  6. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  7. def clone(): AnyRef

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

  8. var coalesce: Int

  9. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  10. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  11. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase

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

    Definition Classes
    AnyRef

  13. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  14. def finalize(): Unit

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

  15. var forceLoadBam: Boolean

  16. var forceLoadFastq: Boolean

  17. var forceLoadIFastq: Boolean

  18. var forceLoadParquet: Boolean

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

    Definition Classes
    AnyRef → Any

  20. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  21. var inputPath: String

  22. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  23. var knownIndelsFile: String

  24. var knownSnpsFile: String

  25. var locallyRealign: Boolean

  26. var lodThreshold: Double

  27. var logLevel: String

    Definition Classes
    ParquetArgs

  28. var markDuplicates: Boolean

  29. var maxConsensusNumber: Int

  30. var maxIndelSize: Int

  31. var maxTargetSize: Int

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

    Definition Classes
    AnyRef

  33. final def notify(): Unit

    Definition Classes
    AnyRef

  34. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  35. var observationsPath: String

  36. var outputPath: String

    Definition Classes
    TransformArgs → SaveArgs

  37. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  38. var printMetrics: Boolean

    Definition Classes
    Args4jBase

  39. var recalibrateBaseQualities: Boolean

  40. var repartition: Int

  41. var sortFastqOutput: Boolean

    Definition Classes
    TransformArgs → ADAMSaveAnyArgs

  42. var sortReads: Boolean

  43. var strictBQSR: 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