c

org.bdgenomics.cannoli.cli

LongMinimap2Args

class LongMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with ParquetArgs

Long read Minimap2 command line arguments.

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.Minimap2Args, ReadGroupArgs, Args4jBase, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. LongMinimap2Args
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. SaveArgs
  5. ParquetRDDArgs
  6. Minimap2Args
  7. ReadGroupArgs
  8. Args4jBase
  9. AnyRef
  10. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new LongMinimap2Args()

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
    Minimap2Args
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    LongMinimap2Args → 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 createReadGroup(): ReadGroup
    Definition Classes
    ReadGroupArgs
  11. var deferMerging: Boolean
    Definition Classes
    LongMinimap2Args → ADAMSaveAnyArgs
  12. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  13. var disableFastConcat: Boolean
    Definition Classes
    LongMinimap2Args → 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 executable: String
    Definition Classes
    Minimap2Args
  18. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  19. var flowOrder: String
    Definition Classes
    ReadGroupArgs
  20. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  21. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  22. var image: String
    Definition Classes
    Minimap2Args
  23. var indexPath: String
    Definition Classes
    Minimap2Args
  24. var inputPath: String
  25. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  26. var keySequence: String
    Definition Classes
    ReadGroupArgs
  27. var library: String
    Definition Classes
    ReadGroupArgs
  28. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  29. var minimap2Args: String
    Definition Classes
    Minimap2Args
  30. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  31. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  32. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  33. var outputPath: String
    Definition Classes
    LongMinimap2Args → SaveArgs
  34. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  35. var platform: String
    Definition Classes
    ReadGroupArgs
  36. var platformModel: String
    Definition Classes
    ReadGroupArgs
  37. var platformUnit: String
    Definition Classes
    ReadGroupArgs
  38. var predictedMedianInsertSize: Integer
    Definition Classes
    ReadGroupArgs
  39. var preset: String
    Definition Classes
    Minimap2Args
  40. var readGroup: ReadGroup
    Definition Classes
    ReadGroupArgs
  41. var readGroupId: String
    Definition Classes
    ReadGroupArgs
  42. var runDate: Long
    Definition Classes
    ReadGroupArgs
  43. var sampleId: String
    Definition Classes
    ReadGroupArgs
  44. var seed: Integer
    Definition Classes
    Minimap2Args
  45. var sequenceDictionary: String
  46. var sequencingCenter: String
    Definition Classes
    ReadGroupArgs
  47. var sortFastqOutput: Boolean
    Definition Classes
    LongMinimap2Args → ADAMSaveAnyArgs
  48. var sudo: Boolean
    Definition Classes
    Minimap2Args
  49. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  50. def toString(): String
    Definition Classes
    AnyRef → Any
  51. var useDocker: Boolean
    Definition Classes
    Minimap2Args
  52. var useSingularity: Boolean
    Definition Classes
    Minimap2Args
  53. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  54. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  55. 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.Minimap2Args

Inherited from ReadGroupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped