class SnpEffArgs extends cannoli.SnpEffArgs with ADAMSaveAnyArgs with ParquetArgs

SnpEff command line arguments.

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

Instance Constructors

  1. new SnpEffArgs()

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. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. var asSingleFile: Boolean
    Definition Classes
    SnpEffArgs → ADAMSaveAnyArgs
  6. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  7. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  8. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  9. var database: String
    Definition Classes
    SnpEffArgs
  10. var deferMerging: Boolean
    Definition Classes
    SnpEffArgs → ADAMSaveAnyArgs
  11. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  12. var disableFastConcat: Boolean
    Definition Classes
    SnpEffArgs → 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
    SnpEffArgs
  17. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  19. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  20. var image: String
    Definition Classes
    SnpEffArgs
  21. var inputPath: String
  22. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  23. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  24. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  25. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  26. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  27. var outputPath: String
    Definition Classes
    SnpEffArgs → SaveArgs
  28. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  29. var sortFastqOutput: Boolean
    Definition Classes
    SnpEffArgs → ADAMSaveAnyArgs
  30. var stringency: String
  31. var sudo: Boolean
    Definition Classes
    SnpEffArgs
  32. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  33. def toString(): String
    Definition Classes
    AnyRef → Any
  34. var useDocker: Boolean
    Definition Classes
    SnpEffArgs
  35. var useSingularity: Boolean
    Definition Classes
    SnpEffArgs
  36. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.SnpEffArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped