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. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

10. var coalesce: Int

11. var compressionCodec: CompressionCodecName

    Definition Classes

    ParquetArgs → ParquetRDDArgs

12. var concatFilename: String

13. var disableDictionaryEncoding: Boolean

    Definition Classes

    ParquetArgs → ParquetRDDArgs

14. var doPrintUsage: Boolean

    Definition Classes

    Args4jBase

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

    Definition Classes

    AnyRef

16. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

17. var fastqRecordGroup: String

18. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

19. var forceLoadBam: Boolean

20. var forceLoadFastq: Boolean

21. var forceLoadIFastq: Boolean

22. var forceLoadParquet: Boolean

23. var forceShuffle: Boolean

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

    Definition Classes

    AnyRef → Any

25. def hashCode(): Int

    Definition Classes

    AnyRef → Any

26. var inputPath: String

27. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

28. var knownIndelsFile: String

29. var knownSnpsFile: String

30. var limitProjection: Boolean

31. var locallyRealign: Boolean

32. var lodThreshold: Double

33. var logLevel: String

    Definition Classes

    ParquetArgs

34. var markDuplicates: Boolean

35. var maxConsensusNumber: Int

36. var maxIndelSize: Int

37. var maxTargetSize: Int

38. var mdTagsFragmentSize: Long

39. var mdTagsOverwrite: Boolean

40. var mdTagsReferenceFile: String

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

    Definition Classes

    AnyRef

42. final def notify(): Unit

    Definition Classes

    AnyRef

43. final def notifyAll(): Unit

    Definition Classes

    AnyRef

44. var observationsPath: String

45. var outputPath: String

    Definition Classes

    TransformArgs → SaveArgs

46. var pageSize: Int

    Definition Classes

    ParquetArgs → ParquetRDDArgs

47. var pairedFastqFile: String

48. var printMetrics: Boolean

    Definition Classes

    Args4jBase

49. var recalibrateBaseQualities: Boolean

50. var repartition: Int

51. var sortFastqOutput: Boolean

    Definition Classes

    TransformArgs → ADAMSaveAnyArgs

52. var sortReads: Boolean

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( ... )