# MagicBlastArgs - Cannoli_2.11: CLI 0.8.0 API - org.bdgenomics.cannoli.cli.MagicBlastArgs
MagicBlastArgs - Cannoli 2.11 CLI 0.8.0 API - org.bdgenomics.cannoli.cli.MagicBlastArgs
Keywords: MagicBlastArgs Cannoli 2.11 CLI 0.8.0 API org.bdgenomics.cannoli.cli.MagicBlastArgs

org.bdgenomics.cannoli.cli

# MagicBlastArgs

###
Related Doc: package cli

#### class MagicBlastArgs extends cannoli.MagicBlastArgs with ADAMSaveAnyArgs with ParquetArgs

Magic-BLAST command line arguments.

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.MagicBlastArgs, Args4jBase, AnyRef, Any
Ordering

1. Alphabetic
2. By Inheritance

Inherited

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

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Visibility

1. Public
2. All

### Instance Constructors

1. #### new MagicBlastArgs()

### 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. #### var addFiles: Boolean

   Definition Classes
     MagicBlastArgs

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

   Definition Classes
     Any

6. #### var asSingleFile: Boolean

   Definition Classes
     MagicBlastArgs → ADAMSaveAnyArgs

7. #### var blockSize: Int

   Definition Classes
     ParquetArgs → ParquetRDDArgs

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

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

9. #### var compressionCodec: CompressionCodecName

   Definition Classes
     ParquetArgs → ParquetRDDArgs

10. #### var db: String

    Definition Classes
      MagicBlastArgs

11. #### var deferMerging: Boolean

    Definition Classes
      MagicBlastArgs → ADAMSaveAnyArgs

12. #### var disableDictionaryEncoding: Boolean

    Definition Classes
      ParquetArgs → ParquetRDDArgs

13. #### var disableFastConcat: Boolean

    Definition Classes
      MagicBlastArgs → 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
      AnyRef → Any

17. #### var executable: String

    Definition Classes
      MagicBlastArgs

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

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

19. #### var gapExtend: Integer

    Definition Classes
      MagicBlastArgs

20. #### var gapOpen: Integer

    Definition Classes
      MagicBlastArgs

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

23. #### var image: String

    Definition Classes
      MagicBlastArgs

24. #### var inputPath: String

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

    Definition Classes
      Any

26. #### var logLevel: String

    Definition Classes
      ParquetArgs

27. #### var maxEditDistance: Integer

    Definition Classes
      MagicBlastArgs

28. #### var maxIntronLength: Integer

    Definition Classes
      MagicBlastArgs

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

32. #### var outputPath: String

    Definition Classes
      MagicBlastArgs → SaveArgs

33. #### var pageSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

34. #### var penalty: Integer

    Definition Classes
      MagicBlastArgs

35. #### var percentIdentity: Double

    Definition Classes
      MagicBlastArgs

36. #### var printMetrics: Boolean

    Definition Classes
      Args4jBase

37. #### var score: String

    Definition Classes
      MagicBlastArgs

38. #### var sortFastqOutput: Boolean

    Definition Classes
      MagicBlastArgs → ADAMSaveAnyArgs

39. #### var stringency: String

    Definition Classes
      MagicBlastArgs

40. #### var sudo: Boolean

    Definition Classes
      MagicBlastArgs

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

43. #### var transcriptome: Boolean

    Definition Classes
      MagicBlastArgs

44. #### var useDocker: Boolean

    Definition Classes
      MagicBlastArgs

45. #### var useSingularity: Boolean

    Definition Classes
      MagicBlastArgs

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

49. #### var wordSize: Integer

    Definition Classes
      MagicBlastArgs

### Inherited from ParquetArgs

### Inherited from ADAMSaveAnyArgs

### Inherited from SaveArgs

### Inherited from ParquetRDDArgs

### Inherited from cannoli.MagicBlastArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped