class BlastnArgs extends cannoli.BlastnArgs with ADAMSaveAnyArgs with ParquetArgs

Blastn command line arguments.

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

Instance Constructors

  1. new BlastnArgs()

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
    BlastnArgs
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    BlastnArgs → ADAMSaveAnyArgs
  7. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  8. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  9. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  10. var db: String
    Definition Classes
    BlastnArgs
  11. var deferMerging: Boolean
    Definition Classes
    BlastnArgs → ADAMSaveAnyArgs
  12. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  13. var disableFastConcat: Boolean
    Definition Classes
    BlastnArgs → 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 evalue: Double
    Definition Classes
    BlastnArgs
  18. var executable: String
    Definition Classes
    BlastnArgs
  19. var gapExtend: Integer
    Definition Classes
    BlastnArgs
  20. var gapOpen: Integer
    Definition Classes
    BlastnArgs
  21. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  22. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  23. var image: String
    Definition Classes
    BlastnArgs
  24. var inputPath: String
  25. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  26. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  27. var maxHsps: Integer
    Definition Classes
    BlastnArgs
  28. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  29. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  30. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  31. var numThreads: Integer
    Definition Classes
    BlastnArgs
  32. var outputPath: String
    Definition Classes
    BlastnArgs → SaveArgs
  33. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  34. var penalty: Integer
    Definition Classes
    BlastnArgs
  35. var percentIdentity: Double
    Definition Classes
    BlastnArgs
  36. var reward: Integer
    Definition Classes
    BlastnArgs
  37. var sortFastqOutput: Boolean
    Definition Classes
    BlastnArgs → ADAMSaveAnyArgs
  38. var stringency: String
    Definition Classes
    BlastnArgs
  39. var sudo: Boolean
    Definition Classes
    BlastnArgs
  40. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  41. def toString(): String
    Definition Classes
    AnyRef → Any
  42. var useDocker: Boolean
    Definition Classes
    BlastnArgs
  43. var useSingularity: Boolean
    Definition Classes
    BlastnArgs
  44. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  45. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  46. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  47. var wordSize: Integer
    Definition Classes
    BlastnArgs

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.BlastnArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped