org.bdgenomics.adam.cli

# TransformArgs

#### class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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Inherited

1. TransformArgs
2. ParquetArgs
3. ADAMSaveAnyArgs
4. SaveArgs
5. ParquetRDDArgs
6. Args4jBase
7. AnyRef
8. Any

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### Instance Constructors

1. #### new 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. #### var cache: Boolean

10. #### def clone(): AnyRef

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

11. #### var coalesce: Int

12. #### var compressionCodec: CompressionCodecName

    Definition Classes
      ParquetArgs → ParquetRDDArgs

13. #### var concatFilename: String

14. #### var deferMerging: Boolean

    Definition Classes
      TransformArgs → ADAMSaveAnyArgs

15. #### var disableDictionaryEncoding: Boolean

    Definition Classes
      ParquetArgs → ParquetRDDArgs

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. #### var fastqRecordGroup: String

20. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

21. #### var forceLoadBam: Boolean

22. #### var forceLoadFastq: Boolean

23. #### var forceLoadIFastq: Boolean

24. #### var forceLoadParquet: Boolean

25. #### var forceShuffle: Boolean

26. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

27. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

28. #### var inputPath: String

29. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

30. #### var knownIndelsFile: String

31. #### var knownSnpsFile: String

32. #### var limitProjection: Boolean

33. #### var locallyRealign: Boolean

34. #### var lodThreshold: Double

35. #### var logLevel: String

    Definition Classes
      ParquetArgs

36. #### var markDuplicates: Boolean

37. #### var maxConsensusNumber: Int

38. #### var maxIndelSize: Int

39. #### var maxReadsPerTarget: Int

40. #### var maxTargetSize: Int

41. #### var mdTagsFragmentSize: Long

42. #### var mdTagsOverwrite: Boolean

43. #### var mdTagsReferenceFile: String

44. #### var minAcceptableQuality: Int

45. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

46. #### final def notify(): Unit

    Definition Classes
      AnyRef

47. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

48. #### var outputPath: String

    Definition Classes
      TransformArgs → SaveArgs

49. #### var pageSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

50. #### var pairedFastqFile: String

51. #### var printMetrics: Boolean

    Definition Classes
      Args4jBase

52. #### var recalibrateBaseQualities: Boolean

53. #### var reference: String

54. #### var repartition: Int

55. #### var sortFastqOutput: Boolean

    Definition Classes
      TransformArgs → ADAMSaveAnyArgs

56. #### var sortLexicographically: Boolean

57. #### var sortReads: Boolean

58. #### var storageLevel: String

59. #### var stringency: String

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

    Definition Classes
      AnyRef

61. #### def toString(): String

    Definition Classes
      AnyRef → Any

62. #### var unclipReads: Boolean

63. #### var useAlignedReadPredicate: Boolean

64. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

66. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from ParquetArgs

### Inherited from ADAMSaveAnyArgs

### Inherited from SaveArgs

### Inherited from ParquetRDDArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped