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

Bwa mem command line arguments.

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

Instance Constructors

  1. new BwaMemArgs()

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

Inherited from ParquetArgs

Inherited from CramArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.BwaMemArgs

Inherited from ReadGroupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

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