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

org.bdgenomics.cannoli.cli

# FreebayesArgs

###
Related Doc: package cli

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

Freebayes command line arguments.

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

1. Alphabetic
2. By Inheritance

Inherited

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

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Visibility

1. Public
2. All

### Instance Constructors

1. #### new FreebayesArgs()

### 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
     FreebayesArgs

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

   Definition Classes
     Any

6. #### var asSingleFile: Boolean

   Definition Classes
     FreebayesArgs → 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 deferMerging: Boolean

    Definition Classes
      FreebayesArgs → ADAMSaveAnyArgs

11. #### var disableDictionaryEncoding: Boolean

    Definition Classes
      ParquetArgs → ParquetRDDArgs

12. #### var disableFastConcat: Boolean

    Definition Classes
      FreebayesArgs → ADAMSaveAnyArgs

13. #### var doPrintUsage: Boolean

    Definition Classes
      Args4jBase

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

16. #### var executable: String

    Definition Classes
      FreebayesArgs

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

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

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

    Definition Classes
      AnyRef → Any

19. #### var gvcf: Boolean

    Definition Classes
      FreebayesArgs

20. #### var gvcfChunk: Int

    Definition Classes
      FreebayesArgs

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

    Definition Classes
      AnyRef → Any

22. #### var image: String

    Definition Classes
      FreebayesArgs

23. #### var inputPath: String

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

    Definition Classes
      Any

25. #### var logLevel: String

    Definition Classes
      ParquetArgs

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

29. #### var outputPath: String

    Definition Classes
      FreebayesArgs → SaveArgs

30. #### var pageSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

31. #### var printMetrics: Boolean

    Definition Classes
      Args4jBase

32. #### var referencePath: String

    Definition Classes
      FreebayesArgs

33. #### var sortFastqOutput: Boolean

    Definition Classes
      FreebayesArgs → ADAMSaveAnyArgs

34. #### var stringency: String

35. #### var sudo: Boolean

    Definition Classes
      FreebayesArgs

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

38. #### var useDocker: Boolean

    Definition Classes
      FreebayesArgs

39. #### var useSingularity: Boolean

    Definition Classes
      FreebayesArgs

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

42. #### 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 cannoli.FreebayesArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped