Class

org.bdgenomics.cannoli.cli

Bowtie2Args

Related Doc: package cli

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class Bowtie2Args extends cannoli.Bowtie2Args with ADAMSaveAnyArgs with ParquetArgs

Bowtie 2 command line arguments.

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.Bowtie2Args, Args4jBase, AnyRef, Any
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Inherited
  1. Bowtie2Args
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. SaveArgs
  5. ParquetRDDArgs
  6. Bowtie2Args
  7. Args4jBase
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Bowtie2Args()

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. var addFiles: Boolean

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    Definition Classes
    Bowtie2Args
  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  6. var asSingleFile: Boolean

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    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs
  7. var blockSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  8. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. var compressionCodec: CompressionCodecName

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  10. var deferMerging: Boolean

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    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs
  11. var disableDictionaryEncoding: Boolean

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  12. var disableFastConcat: Boolean

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    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs
  13. var doPrintUsage: Boolean

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    Definition Classes
    Args4jBase
  14. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  16. var executable: String

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    Definition Classes
    Bowtie2Args
  17. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  19. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  20. var image: String

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    Definition Classes
    Bowtie2Args
  21. var indexPath: String

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    Definition Classes
    Bowtie2Args
  22. var inputPath: String

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  23. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  24. var logLevel: String

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    Definition Classes
    ParquetArgs
  25. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  26. final def notify(): Unit

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    Definition Classes
    AnyRef
  27. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  28. var outputPath: String

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    Definition Classes
    Bowtie2Args → SaveArgs
  29. var pageSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  30. var printMetrics: Boolean

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    Definition Classes
    Args4jBase
  31. var sortFastqOutput: Boolean

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    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs
  32. var stringency: String

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  33. var sudo: Boolean

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    Definition Classes
    Bowtie2Args
  34. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  35. def toString(): String

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    Definition Classes
    AnyRef → Any
  36. var useDocker: Boolean

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    Definition Classes
    Bowtie2Args
  37. var useSingularity: Boolean

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    Definition Classes
    Bowtie2Args
  38. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  39. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  40. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.Bowtie2Args

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

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