TrioGenotyperArgs

Value Members

1. final def !=(arg0: Any): Boolean

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

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

   

   Definition Classes

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4. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

5. var asSingleFile: Boolean

   

   Definition Classes

   TrioGenotyperArgs → ADAMSaveAnyArgs

6. var autosomalOnly: Boolean

   

   Definition Classes

   TrioGenotyperArgs → PrefilterReadsArgs

7. var blockSize: Int

   

   Definition Classes

   ParquetArgs → ParquetRDDArgs

8. var childPath: String

   

9. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

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   Annotations

   @throws( ... )

10. var compressionCodec: CompressionCodecName

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

11. var deferMerging: Boolean

    

    Definition Classes

    TrioGenotyperArgs → ADAMSaveAnyArgs

12. var disableDictionaryEncoding: Boolean

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

13. var disableFastConcat: Boolean

    

    Definition Classes

    TrioGenotyperArgs → ADAMSaveAnyArgs

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

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17. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

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    Annotations

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

18. var firstParentPath: String

    

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

    

    Definition Classes

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20. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

21. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

22. var isNotGrc: Boolean

    

23. var keepDuplicates: Boolean

    

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

24. var keepMitochondrialChromosome: Boolean

    

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

25. var keepNonPrimary: Boolean

    

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

26. var logLevel: String

    

    Definition Classes

    ParquetArgs

27. var maxHetIndelAltAllelicFraction: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

28. var maxHetSnpAltAllelicFraction: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

29. var maxIndelDepth: Int

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

30. var maxIndelPhredStrandBias: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

31. var maxSnpDepth: Int

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

32. var maxSnpPhredStrandBias: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

33. var minHetIndelAltAllelicFraction: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

34. var minHetIndelQualityByDepth: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

35. var minHetSnpAltAllelicFraction: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

36. var minHetSnpQualityByDepth: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

37. var minHomIndelAltAllelicFraction: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

38. var minHomIndelQualityByDepth: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

39. var minHomSnpAltAllelicFraction: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

40. var minHomSnpQualityByDepth: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

41. var minIndelDepth: Int

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

42. var minIndelRMSMappingQuality: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

43. var minMappingQuality: Int

    

    Definition Classes

    TrioGenotyperArgs → PrefilterReadsArgs

44. var minObservationsForDiscovery: Int

    

45. var minPhredForDiscovery: Int

    

46. var minQuality: Int

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

47. var minSnpDepth: Int

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

48. var minSnpRMSMappingQuality: Float

    

    Definition Classes

    TrioGenotyperArgs → HardFilterGenotypesArgs

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

    

    Definition Classes

    AnyRef

50. final def notify(): Unit

    

    Definition Classes

    AnyRef

51. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

52. var outputPath: String

    

    Definition Classes

    TrioGenotyperArgs → SaveArgs

53. var pageSize: Int

    

    Definition Classes

    ParquetArgs → ParquetRDDArgs

54. var ploidy: Int

    

55. var printMetrics: Boolean

    

    Definition Classes

    Args4jBase

56. var secondParentPath: String

    

57. var sortFastqOutput: Boolean

    

    Definition Classes

    TrioGenotyperArgs → ADAMSaveAnyArgs

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

    

    Definition Classes

    AnyRef

59. def toString(): String

    

    Definition Classes

    AnyRef → Any

60. var variantsToCall: String

    

61. final def wait(): Unit

    

    Definition Classes

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    Annotations

    @throws( ... )

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

    

    Definition Classes

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    Annotations

    @throws( ... )

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

    

    Definition Classes

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    Annotations

    @throws( ... )