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 asSingleFile: Boolean

   Definition Classes

   TransformArgs → ADAMSaveAnyArgs

8. var blockSize: Int

   Definition Classes

   ParquetArgs → ParquetRDDArgs

9. var cache: Boolean

10. def clone(): AnyRef

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

11. var coalesce: Int

12. var compressionCodec: CompressionCodecName

    Definition Classes

    ParquetArgs → ParquetRDDArgs

13. var concatFilename: String

14. var disableDictionaryEncoding: Boolean

    Definition Classes

    ParquetArgs → ParquetRDDArgs

15. var doPrintUsage: Boolean

    Definition Classes

    Args4jBase

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

    Definition Classes

    AnyRef

17. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

18. var fastqRecordGroup: String

19. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

20. var forceLoadBam: Boolean

21. var forceLoadFastq: Boolean

22. var forceLoadIFastq: Boolean

23. var forceLoadParquet: Boolean

24. var forceShuffle: Boolean

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

    Definition Classes

    AnyRef → Any

26. def hashCode(): Int

    Definition Classes

    AnyRef → Any

27. var inputPath: String

28. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

29. var knownIndelsFile: String

30. var knownSnpsFile: String

31. var limitProjection: Boolean

32. var locallyRealign: Boolean

33. var lodThreshold: Double

34. var logLevel: String

    Definition Classes

    ParquetArgs

35. var markDuplicates: Boolean

36. var maxConsensusNumber: Int

37. var maxIndelSize: Int

38. var maxTargetSize: Int

39. var mdTagsFragmentSize: Long

40. var mdTagsOverwrite: Boolean

41. var mdTagsReferenceFile: String

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

    Definition Classes

    AnyRef

43. final def notify(): Unit

    Definition Classes

    AnyRef

44. final def notifyAll(): Unit

    Definition Classes

    AnyRef

45. var observationsPath: String

46. var outputPath: String

    Definition Classes

    TransformArgs → SaveArgs

47. var pageSize: Int

    Definition Classes

    ParquetArgs → ParquetRDDArgs

48. var pairedFastqFile: String

49. var printMetrics: Boolean

    Definition Classes

    Args4jBase

50. var recalibrateBaseQualities: Boolean

51. var repartition: Int

52. var sortFastqOutput: Boolean

    Definition Classes

    TransformArgs → ADAMSaveAnyArgs

53. var sortReads: Boolean

54. var storageLevel: String

55. var stringency: String

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

    Definition Classes

    AnyRef

57. def toString(): String

    Definition Classes

    AnyRef → Any

58. var useAlignedReadPredicate: Boolean

59. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )