org.bdgenomics.cannoli.cli

Bowtie2Args

class Bowtie2Args extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

  1. new Bowtie2Args()

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. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. var asSingleFile: Boolean

    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs

  8. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  9. var bowtie2Path: String

  10. def clone(): AnyRef

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

  11. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  12. var deferMerging: Boolean

    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs

  13. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  14. var disableFastConcat: Boolean

    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs

  15. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase

  16. var dockerImage: String

  17. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  18. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  19. def finalize(): Unit

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

  20. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  21. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  22. var indexPath: String

  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
    Bowtie2Args → SaveArgs

  30. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  31. var printMetrics: Boolean

    Definition Classes
    Args4jBase

  32. var sortFastqOutput: Boolean

    Definition Classes
    Bowtie2Args → ADAMSaveAnyArgs

  33. var stringency: String

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

    Definition Classes
    AnyRef

  35. def toString(): String

    Definition Classes
    AnyRef → Any

  36. var useDocker: Boolean

  37. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  39. 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