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. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

8. var coalesce: Int

   

9. var compressionCodec: CompressionCodecName

   

   Definition Classes

   ParquetArgs → ParquetRDDArgs

10. var concatFilename: String

    

11. var disableDictionaryEncoding: Boolean

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

12. var doPrintUsage: Boolean

    

    Definition Classes

    Args4jBase

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

    

    Definition Classes

    AnyRef

14. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

15. var fastqRecordGroup: String

    

16. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

17. var forceLoadBam: Boolean

    

18. var forceLoadFastq: Boolean

    

19. var forceLoadIFastq: Boolean

    

20. var forceLoadParquet: Boolean

    

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

    

    Definition Classes

    AnyRef → Any

22. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

23. var inputPath: String

    

24. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

25. var knownIndelsFile: String

    

26. var knownSnpsFile: String

    

27. var limitProjection: Boolean

    

28. var locallyRealign: Boolean

    

29. var lodThreshold: Double

    

30. var logLevel: String

    

    Definition Classes

    ParquetArgs

31. var markDuplicates: Boolean

    

32. var maxConsensusNumber: Int

    

33. var maxIndelSize: Int

    

34. var maxTargetSize: Int

    

35. var mdTagsFragmentSize: Long

    

36. var mdTagsOverwrite: Boolean

    

37. var mdTagsReferenceFile: String

    

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

    

    Definition Classes

    AnyRef

39. final def notify(): Unit

    

    Definition Classes

    AnyRef

40. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

41. var observationsPath: String

    

42. var outputPath: String

    

    Definition Classes

    TransformArgs → SaveArgs

43. var pageSize: Int

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

44. var pairedFastqFile: String

    

45. var printMetrics: Boolean

    

    Definition Classes

    Args4jBase

46. var recalibrateBaseQualities: Boolean

    

47. var repartition: Int

    

48. var sortFastqOutput: Boolean

    

    Definition Classes

    TransformArgs → ADAMSaveAnyArgs

49. var sortReads: Boolean

    

50. var stringency: String

    

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

    

    Definition Classes

    AnyRef

52. def toString(): String

    

    Definition Classes

    AnyRef → Any

53. var useAlignedReadPredicate: Boolean

    

54. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )