TrioGenotyperArgs

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

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5. final def ==(arg0: Any): Boolean

   Definition Classes

   Any

6. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7. var asSingleFile: Boolean

   Definition Classes

   TrioGenotyperArgs → ADAMSaveAnyArgs

8. var autosomalOnly: Boolean

   Definition Classes

   TrioGenotyperArgs → PrefilterReadsArgs

9. var blockSize: Int

   Definition Classes

   ParquetArgs → ParquetRDDArgs

10. var childPath: String

11. def clone(): AnyRef

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

12. var compressionCodec: CompressionCodecName

    Definition Classes

    ParquetArgs → ParquetRDDArgs

13. var deferMerging: Boolean

    Definition Classes

    TrioGenotyperArgs → ADAMSaveAnyArgs

14. var disableDictionaryEncoding: Boolean

    Definition Classes

    ParquetArgs → ParquetRDDArgs

15. var disableFastConcat: Boolean

    Definition Classes

    TrioGenotyperArgs → ADAMSaveAnyArgs

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. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

20. var firstParentPath: String

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

    Definition Classes

    AnyRef → Any

22. def hashCode(): Int

    Definition Classes

    AnyRef → Any

23. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

24. var isNotGrc: Boolean

25. var keepDuplicates: Boolean

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

26. var keepMitochondrialChromosome: Boolean

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

27. var keepNonPrimary: Boolean

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

28. var logLevel: String

    Definition Classes

    ParquetArgs

29. var maxHetIndelAltAllelicFraction: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

30. var maxHetSnpAltAllelicFraction: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

31. var maxIndelDepth: Int

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

32. var maxIndelPhredStrandBias: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

33. var maxSnpDepth: Int

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

34. var maxSnpPhredStrandBias: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

35. var minHetIndelAltAllelicFraction: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

36. var minHetIndelQualityByDepth: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

37. var minHetSnpAltAllelicFraction: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

38. var minHetSnpQualityByDepth: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

39. var minHomIndelAltAllelicFraction: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

40. var minHomIndelQualityByDepth: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

41. var minHomSnpAltAllelicFraction: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

42. var minHomSnpQualityByDepth: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

43. var minIndelDepth: Int

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

44. var minIndelRMSMappingQuality: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

45. var minMappingQuality: Int

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

46. var minObservationsForDiscovery: Int

47. var minPhredForDiscovery: Int

48. var minQuality: Int

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

49. var minSnpDepth: Int

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

50. var minSnpRMSMappingQuality: Float

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

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

    Definition Classes

    AnyRef

52. final def notify(): Unit

    Definition Classes

    AnyRef

53. final def notifyAll(): Unit

    Definition Classes

    AnyRef

54. var outputPath: String

    Definition Classes

    TrioGenotyperArgs → SaveArgs

55. var pageSize: Int

    Definition Classes

    ParquetArgs → ParquetRDDArgs

56. var ploidy: Int

57. var printMetrics: Boolean

    Definition Classes

    Args4jBase

58. var secondParentPath: String

59. var sortFastqOutput: Boolean

    Definition Classes

    TrioGenotyperArgs → ADAMSaveAnyArgs

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

    Definition Classes

    AnyRef

61. def toString(): String

    Definition Classes

    AnyRef → Any

62. var variantsToCall: String

63. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

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    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )