org.bdgenomics.adam.cli

TransformArgs

class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, ADAMSaveArgs, ADAMParquetArgs, Args4jBase, AnyRef, Any
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Inherited
  1. TransformArgs
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. ADAMSaveArgs
  5. ADAMParquetArgs
  6. Args4jBase
  7. AnyRef
  8. Any
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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 → ADAMParquetArgs

  8. def clone(): AnyRef

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

  9. var coalesce: Int

  10. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ADAMParquetArgs

  11. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ADAMParquetArgs

  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. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  17. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  18. var inputPath: String

  19. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  20. var knownIndelsFile: String

  21. var knownSnpsFile: String

  22. var locallyRealign: Boolean

  23. var lodThreshold: Double

  24. var logLevel: String

    Definition Classes
    ParquetArgs

  25. var markDuplicates: Boolean

  26. var maxConsensusNumber: Int

  27. var maxIndelSize: Int

  28. var maxTargetSize: Int

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

    Definition Classes
    AnyRef

  30. final def notify(): Unit

    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  32. var observationsPath: String

  33. var outputPath: String

    Definition Classes
    TransformArgs → ADAMSaveArgs

  34. var pageSize: Int

    Definition Classes
    ParquetArgs → ADAMParquetArgs

  35. var printMetrics: Boolean

    Definition Classes
    Args4jBase

  36. var qualityBasedTrim: Boolean

  37. var qualityThreshold: Int

  38. var recalibrateBaseQualities: Boolean

  39. var repartition: Int

  40. var sortFastqOutput: Boolean

    Definition Classes
    TransformArgs → ADAMSaveAnyArgs

  41. var sortReads: Boolean

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

    Definition Classes
    AnyRef

  43. def toString(): String

    Definition Classes
    AnyRef → Any

  44. var trimBeforeBQSR: Boolean

  45. var trimEnd: Int

  46. var trimReadGroup: String

  47. var trimReads: Boolean

  48. var trimStart: Int

  49. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from ADAMSaveArgs

Inherited from ADAMParquetArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped