c

org.bdgenomics.cannoli.cli

MagicBlastArgs

class MagicBlastArgs extends cannoli.MagicBlastArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Magic-BLAST command line arguments.

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

Instance Constructors

  1. new MagicBlastArgs()

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
    MagicBlastArgs
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    MagicBlastArgs → ADAMSaveAnyArgs
  7. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  8. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  9. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  10. def configureCramFormat(sc: SparkContext): Option[Unit]

    Configure CRAM format.

    Configure CRAM format.

    sc

    Spark context to configure

    Definition Classes
    CramArgs
  11. val cramReference: String
    Definition Classes
    CramArgs
    Annotations
    @Option()
  12. var db: String
    Definition Classes
    MagicBlastArgs
  13. var deferMerging: Boolean
    Definition Classes
    MagicBlastArgs → ADAMSaveAnyArgs
  14. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  15. var disableFastConcat: Boolean
    Definition Classes
    MagicBlastArgs → ADAMSaveAnyArgs
  16. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  17. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  18. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  19. var executable: String
    Definition Classes
    MagicBlastArgs
  20. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  21. var gapExtend: Integer
    Definition Classes
    MagicBlastArgs
  22. var gapOpen: Integer
    Definition Classes
    MagicBlastArgs
  23. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  24. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  25. var image: String
    Definition Classes
    MagicBlastArgs
  26. var inputPath: String
  27. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  28. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  29. var maxEditDistance: Integer
    Definition Classes
    MagicBlastArgs
  30. var maxIntronLength: Integer
    Definition Classes
    MagicBlastArgs
  31. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  32. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  33. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  34. var outputPath: String
    Definition Classes
    MagicBlastArgs → SaveArgs
  35. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  36. var penalty: Integer
    Definition Classes
    MagicBlastArgs
  37. var percentIdentity: Double
    Definition Classes
    MagicBlastArgs
  38. var score: String
    Definition Classes
    MagicBlastArgs
  39. var sortFastqOutput: Boolean
    Definition Classes
    MagicBlastArgs → ADAMSaveAnyArgs
  40. var stringency: String
    Definition Classes
    MagicBlastArgs
  41. var sudo: Boolean
    Definition Classes
    MagicBlastArgs
  42. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  43. def toString(): String
    Definition Classes
    AnyRef → Any
  44. var transcriptome: Boolean
    Definition Classes
    MagicBlastArgs
  45. var useDocker: Boolean
    Definition Classes
    MagicBlastArgs
  46. var useSingularity: Boolean
    Definition Classes
    MagicBlastArgs
  47. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  48. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  49. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  50. var wordSize: Integer
    Definition Classes
    MagicBlastArgs

Inherited from ParquetArgs

Inherited from CramArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.MagicBlastArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped