org.bdgenomics.adam.cli

# TransformArgs

###
Related Doc: package cli

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

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

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2. By Inheritance

Inherited

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

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Visibility

1. Public
2. All

### Instance Constructors

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

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

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

9. #### var coalesce: Int

10. #### var compressionCodec: CompressionCodecName

    Definition Classes
      ParquetArgs → ParquetRDDArgs

11. #### var concatFilename: String

12. #### var deferMerging: Boolean

    Definition Classes
      TransformArgs → ADAMSaveAnyArgs

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. #### var forceShuffle: Boolean

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

26. #### var inputPath: String

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

    Definition Classes
      Any

28. #### var knownIndelsFile: String

29. #### var knownSnpsFile: String

30. #### var limitProjection: Boolean

31. #### var locallyRealign: Boolean

32. #### var lodThreshold: Double

33. #### var logLevel: String

    Definition Classes
      ParquetArgs

34. #### var markDuplicates: Boolean

35. #### var maxConsensusNumber: Int

36. #### var maxIndelSize: Int

37. #### var maxReadsPerTarget: Int

38. #### var maxTargetSize: Int

39. #### var mdTagsFragmentSize: Long

40. #### var mdTagsOverwrite: Boolean

41. #### var mdTagsReferenceFile: String

42. #### var minAcceptableQuality: Int

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

46. #### var outputPath: String

    Definition Classes
      TransformArgs → SaveArgs

47. #### var pageSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

48. #### var pairedFastqFile: String

49. #### var printMetrics: Boolean

    Definition Classes
      Args4jBase

50. #### var recalibrateBaseQualities: Boolean

51. #### var reference: String

52. #### var repartition: Int

53. #### var sortFastqOutput: Boolean

    Definition Classes
      TransformArgs → ADAMSaveAnyArgs

54. #### var sortLexicographically: Boolean

55. #### var sortReads: Boolean

56. #### var storageLevel: String

57. #### var stringency: String

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

60. #### var unclipReads: Boolean

61. #### var useAlignedReadPredicate: Boolean

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

64. #### 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