class BwaMem2Args extends cannoli.BwaMem2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Bwa-mem2 command line arguments.

Linear Supertypes
ParquetArgs, CramArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.BwaMem2Args, ReadGroupArgs, Args4jBase, AnyRef, Any
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  1. Alphabetic
  2. By Inheritance
Inherited
  1. BwaMem2Args
  2. ParquetArgs
  3. CramArgs
  4. ADAMSaveAnyArgs
  5. SaveArgs
  6. ParquetRDDArgs
  7. BwaMem2Args
  8. ReadGroupArgs
  9. Args4jBase
  10. AnyRef
  11. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new BwaMem2Args()

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
    BwaMem2Args
  5. var asFragments: Boolean
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. var asSingleFile: Boolean
    Definition Classes
    BwaMem2Args → ADAMSaveAnyArgs
  8. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  9. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  10. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  11. def configureCramFormat(sc: SparkContext): Option[Unit]

    Configure CRAM format.

    Configure CRAM format.

    sc

    Spark context to configure

    Definition Classes
    CramArgs
  12. val cramReference: String
    Definition Classes
    CramArgs
    Annotations
    @Option()
  13. def createReadGroup(): ReadGroup
    Definition Classes
    ReadGroupArgs
  14. var deferMerging: Boolean
    Definition Classes
    BwaMem2Args → ADAMSaveAnyArgs
  15. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  16. var disableFastConcat: Boolean
    Definition Classes
    BwaMem2Args → ADAMSaveAnyArgs
  17. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  18. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  19. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  20. var executable: String
    Definition Classes
    BwaMem2Args
  21. var flowOrder: String
    Definition Classes
    ReadGroupArgs
  22. var forceLoadIfastq: Boolean
  23. var forceLoadParquet: Boolean
  24. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  25. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  26. var image: String
    Definition Classes
    BwaMem2Args
  27. var indexPath: String
    Definition Classes
    BwaMem2Args
  28. var inputPath: String
  29. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  30. var keySequence: String
    Definition Classes
    ReadGroupArgs
  31. var library: String
    Definition Classes
    ReadGroupArgs
  32. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  33. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  34. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  35. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  36. var outputPath: String
    Definition Classes
    BwaMem2Args → SaveArgs
  37. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  38. var platform: String
    Definition Classes
    ReadGroupArgs
  39. var platformModel: String
    Definition Classes
    ReadGroupArgs
  40. var platformUnit: String
    Definition Classes
    ReadGroupArgs
  41. var predictedMedianInsertSize: Integer
    Definition Classes
    ReadGroupArgs
  42. var readGroup: ReadGroup
    Definition Classes
    ReadGroupArgs
  43. var readGroupId: String
    Definition Classes
    ReadGroupArgs
  44. var runDate: Long
    Definition Classes
    ReadGroupArgs
  45. var sampleId: String
    Definition Classes
    ReadGroupArgs
  46. var sequenceDictionary: String
  47. var sequencingCenter: String
    Definition Classes
    ReadGroupArgs
  48. var sortFastqOutput: Boolean
    Definition Classes
    BwaMem2Args → ADAMSaveAnyArgs
  49. var stringency: String
  50. var sudo: Boolean
    Definition Classes
    BwaMem2Args
  51. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  52. def toString(): String
    Definition Classes
    AnyRef → Any
  53. var useDocker: Boolean
    Definition Classes
    BwaMem2Args
  54. var useSingularity: Boolean
    Definition Classes
    BwaMem2Args
  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.BwaMem2Args

Inherited from ReadGroupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped