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. 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 stringency: String

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

    Definition Classes

    AnyRef

54. def toString(): String

    Definition Classes

    AnyRef → Any

55. var useAlignedReadPredicate: Boolean

56. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )