c

org.bdgenomics.cannoli.cli

SingleEndUnimapArgs

class SingleEndUnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Single-end read Unimap command line arguments.

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

Instance Constructors

  1. new SingleEndUnimapArgs()

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
    UnimapArgs
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    SingleEndUnimapArgs → 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. 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. def createReadGroup(): ReadGroup
    Definition Classes
    ReadGroupArgs
  13. var deferMerging: Boolean
    Definition Classes
    SingleEndUnimapArgs → ADAMSaveAnyArgs
  14. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  15. var disableFastConcat: Boolean
    Definition Classes
    SingleEndUnimapArgs → 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
    UnimapArgs
  20. var flowOrder: String
    Definition Classes
    ReadGroupArgs
  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
    UnimapArgs
  24. var indexPath: String
    Definition Classes
    UnimapArgs
  25. var inputPath: String
  26. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  27. var keySequence: String
    Definition Classes
    ReadGroupArgs
  28. var library: String
    Definition Classes
    ReadGroupArgs
  29. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  30. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  31. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  32. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  33. var outputPath: String
    Definition Classes
    SingleEndUnimapArgs → 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
    UnimapArgs
  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
    UnimapArgs
  45. var sequenceDictionary: String
  46. var sequencingCenter: String
    Definition Classes
    ReadGroupArgs
  47. var sortFastqOutput: Boolean
    Definition Classes
    SingleEndUnimapArgs → ADAMSaveAnyArgs
  48. var stringency: String
  49. var sudo: Boolean
    Definition Classes
    UnimapArgs
  50. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  51. def toString(): String
    Definition Classes
    AnyRef → Any
  52. var unimapArgs: String
    Definition Classes
    UnimapArgs
  53. var useDocker: Boolean
    Definition Classes
    UnimapArgs
  54. var useSingularity: Boolean
    Definition Classes
    UnimapArgs
  55. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  56. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  57. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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 CramArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.UnimapArgs

Inherited from ReadGroupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped