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. var cache: Boolean

   

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 concatFilename: String

    

12. var disableDictionaryEncoding: Boolean

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

13. var doPrintUsage: Boolean

    

    Definition Classes

    Args4jBase

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

    

    Definition Classes

    AnyRef

15. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

16. var fastqRecordGroup: String

    

17. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

18. var forceLoadBam: Boolean

    

19. var forceLoadFastq: Boolean

    

20. var forceLoadIFastq: Boolean

    

21. var forceLoadParquet: Boolean

    

22. var forceShuffle: Boolean

    

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

    

    Definition Classes

    AnyRef → Any

24. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

25. var inputPath: String

    

26. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

27. var knownIndelsFile: String

    

28. var knownSnpsFile: String

    

29. var limitProjection: Boolean

    

30. var locallyRealign: Boolean

    

31. var lodThreshold: Double

    

32. var logLevel: String

    

    Definition Classes

    ParquetArgs

33. var markDuplicates: Boolean

    

34. var maxConsensusNumber: Int

    

35. var maxIndelSize: Int

    

36. var maxTargetSize: Int

    

37. var mdTagsFragmentSize: Long

    

38. var mdTagsOverwrite: Boolean

    

39. var mdTagsReferenceFile: String

    

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

    

    Definition Classes

    AnyRef

41. final def notify(): Unit

    

    Definition Classes

    AnyRef

42. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

43. var observationsPath: String

    

44. var outputPath: String

    

    Definition Classes

    TransformArgs → SaveArgs

45. var pageSize: Int

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

46. var pairedFastqFile: String

    

47. var printMetrics: Boolean

    

    Definition Classes

    Args4jBase

48. var recalibrateBaseQualities: Boolean

    

49. var repartition: Int

    

50. var sortFastqOutput: Boolean

    

    Definition Classes

    TransformArgs → ADAMSaveAnyArgs

51. var sortReads: Boolean

    

52. var storageLevel: String

    

53. var stringency: String

    

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

    

    Definition Classes

    AnyRef

55. def toString(): String

    

    Definition Classes

    AnyRef → Any

56. var useAlignedReadPredicate: Boolean

    

57. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )