# SingleEndBowtie2Args - Cannoli_2.11: CLI 0.8.0 API - org.bdgenomics.cannoli.cli.SingleEndBowtie2Args
SingleEndBowtie2Args - Cannoli 2.11 CLI 0.8.0 API - org.bdgenomics.cannoli.cli.SingleEndBowtie2Args
Keywords: SingleEndBowtie2Args Cannoli 2.11 CLI 0.8.0 API org.bdgenomics.cannoli.cli.SingleEndBowtie2Args

org.bdgenomics.cannoli.cli

# SingleEndBowtie2Args

###
Related Doc: package cli

#### class SingleEndBowtie2Args extends cannoli.SingleEndBowtie2Args with ADAMSaveAnyArgs with ParquetArgs

Single-end read Bowtie 2 command line arguments.

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.SingleEndBowtie2Args, Args4jBase, AnyRef, Any
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Inherited

1. SingleEndBowtie2Args
2. ParquetArgs
3. ADAMSaveAnyArgs
4. SaveArgs
5. ParquetRDDArgs
6. SingleEndBowtie2Args
7. Args4jBase
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1. #### new SingleEndBowtie2Args()

### 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
     SingleEndBowtie2Args

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

   Definition Classes
     Any

6. #### var asSingleFile: Boolean

   Definition Classes
     SingleEndBowtie2Args → ADAMSaveAnyArgs

7. #### var blockSize: Int

   Definition Classes
     ParquetArgs → ParquetRDDArgs

8. #### var bowtie2Args: String

   Definition Classes
     SingleEndBowtie2Args

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

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

10. #### var compressionCodec: CompressionCodecName

    Definition Classes
      ParquetArgs → ParquetRDDArgs

11. #### var deferMerging: Boolean

    Definition Classes
      SingleEndBowtie2Args → ADAMSaveAnyArgs

12. #### var disableDictionaryEncoding: Boolean

    Definition Classes
      ParquetArgs → ParquetRDDArgs

13. #### var disableFastConcat: Boolean

    Definition Classes
      SingleEndBowtie2Args → 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
      SingleEndBowtie2Args

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

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

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

21. #### var image: String

    Definition Classes
      SingleEndBowtie2Args

22. #### var indexPath: String

    Definition Classes
      SingleEndBowtie2Args

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
      SingleEndBowtie2Args → SaveArgs

30. #### var pageSize: Int

    Definition Classes
      ParquetArgs → ParquetRDDArgs

31. #### var printMetrics: Boolean

    Definition Classes
      Args4jBase

32. #### var sortFastqOutput: Boolean

    Definition Classes
      SingleEndBowtie2Args → ADAMSaveAnyArgs

33. #### var stringency: String

34. #### var sudo: Boolean

    Definition Classes
      SingleEndBowtie2Args

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

37. #### var useDocker: Boolean

    Definition Classes
      SingleEndBowtie2Args

38. #### var useSingularity: Boolean

    Definition Classes
      SingleEndBowtie2Args

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

41. #### 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.SingleEndBowtie2Args

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped