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 deferMerging: Boolean

    Definition Classes

    TransformArgs → ADAMSaveAnyArgs

15. var disableDictionaryEncoding: Boolean

    Definition Classes

    ParquetArgs → ParquetRDDArgs

16. var doPrintUsage: Boolean

    Definition Classes

    Args4jBase

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

    Definition Classes

    AnyRef

18. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

19. var fastqRecordGroup: String

20. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

21. var forceLoadBam: Boolean

22. var forceLoadFastq: Boolean

23. var forceLoadIFastq: Boolean

24. var forceLoadParquet: Boolean

25. var forceShuffle: Boolean

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

    Definition Classes

    AnyRef → Any

27. def hashCode(): Int

    Definition Classes

    AnyRef → Any

28. var inputPath: String

29. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

30. var knownIndelsFile: String

31. var knownSnpsFile: String

32. var limitProjection: Boolean

33. var locallyRealign: Boolean

34. var lodThreshold: Double

35. var logLevel: String

    Definition Classes

    ParquetArgs

36. var markDuplicates: Boolean

37. var maxConsensusNumber: Int

38. var maxIndelSize: Int

39. var maxReadsPerTarget: Int

40. var maxTargetSize: Int

41. var mdTagsFragmentSize: Long

42. var mdTagsOverwrite: Boolean

43. var mdTagsReferenceFile: String

44. var minAcceptableQuality: Int

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

    Definition Classes

    AnyRef

46. final def notify(): Unit

    Definition Classes

    AnyRef

47. final def notifyAll(): Unit

    Definition Classes

    AnyRef

48. var outputPath: String

    Definition Classes

    TransformArgs → SaveArgs

49. var pageSize: Int

    Definition Classes

    ParquetArgs → ParquetRDDArgs

50. var pairedFastqFile: String

51. var printMetrics: Boolean

    Definition Classes

    Args4jBase

52. var recalibrateBaseQualities: Boolean

53. var reference: String

54. var repartition: Int

55. var sortFastqOutput: Boolean

    Definition Classes

    TransformArgs → ADAMSaveAnyArgs

56. var sortLexicographically: Boolean

57. var sortReads: Boolean

58. var storageLevel: String

59. var stringency: String

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

    Definition Classes

    AnyRef

61. def toString(): String

    Definition Classes

    AnyRef → Any

62. var unclipReads: Boolean

63. var useAlignedReadPredicate: Boolean

64. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )