org.bdgenomics.cannoli.cli

# BwaArgs

#### class BwaArgs 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. BwaArgs
2. ParquetArgs
3. ADAMSaveAnyArgs
4. SaveArgs
5. ParquetRDDArgs
6. Args4jBase
7. AnyRef
8. Any

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### Instance Constructors

1. #### new BwaArgs()

### 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. #### var addIndices: Boolean

7. #### var asFragments: Boolean

8. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

9. #### var asSingleFile: Boolean

   Definition Classes
     BwaArgs → ADAMSaveAnyArgs

10. #### var blockSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

11. #### var bwaPath: String

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

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

13. #### var compressionCodec: CompressionCodecName

    Definition Classes
      ParquetArgs → ParquetRDDArgs

14. #### var deferMerging: Boolean

    Definition Classes
      BwaArgs → ADAMSaveAnyArgs

15. #### var disableDictionaryEncoding: Boolean

    Definition Classes
      ParquetArgs → ParquetRDDArgs

16. #### var disableFastConcat: Boolean

    Definition Classes
      BwaArgs → ADAMSaveAnyArgs

17. #### var doPrintUsage: Boolean

    Definition Classes
      Args4jBase

18. #### var dockerCmd: String

19. #### var dockerImage: String

20. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

21. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

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

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

23. #### var forceLoadIfastq: Boolean

24. #### var forceLoadParquet: Boolean

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

27. #### var indexPath: String

28. #### var inputPath: String

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

    Definition Classes
      Any

30. #### var logLevel: String

    Definition Classes
      ParquetArgs

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

34. #### var outputPath: String

    Definition Classes
      BwaArgs → SaveArgs

35. #### var pageSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

36. #### var printMetrics: Boolean

    Definition Classes
      Args4jBase

37. #### var sample: String

38. #### var sequenceDictionary: String

39. #### var sortFastqOutput: Boolean

    Definition Classes
      BwaArgs → ADAMSaveAnyArgs

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

42. #### var useDocker: Boolean

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

45. #### 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