c

org.bdgenomics.cannoli.cli

SingleEndBwaMem2Args

class SingleEndBwaMem2Args extends cannoli.BwaMem2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Single-end read Bwa-mem2 command line arguments.

Linear Supertypes
ParquetArgs, CramArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.BwaMem2Args, ReadGroupArgs, Args4jBase, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SingleEndBwaMem2Args
  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 SingleEndBwaMem2Args()

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. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    SingleEndBwaMem2Args → 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. def createReadGroup(): ReadGroup
    Definition Classes
    ReadGroupArgs
  13. var deferMerging: Boolean
    Definition Classes
    SingleEndBwaMem2Args → ADAMSaveAnyArgs
  14. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  15. var disableFastConcat: Boolean
    Definition Classes
    SingleEndBwaMem2Args → 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
    BwaMem2Args
  20. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  21. var flowOrder: String
    Definition Classes
    ReadGroupArgs
  22. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  23. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  24. var image: String
    Definition Classes
    BwaMem2Args
  25. var indexPath: String
    Definition Classes
    BwaMem2Args
  26. var inputPath: String
  27. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  28. var keySequence: String
    Definition Classes
    ReadGroupArgs
  29. var library: String
    Definition Classes
    ReadGroupArgs
  30. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  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
    SingleEndBwaMem2Args → SaveArgs
  35. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  36. var platform: String
    Definition Classes
    ReadGroupArgs
  37. var platformModel: String
    Definition Classes
    ReadGroupArgs
  38. var platformUnit: String
    Definition Classes
    ReadGroupArgs
  39. var predictedMedianInsertSize: Integer
    Definition Classes
    ReadGroupArgs
  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 sequenceDictionary: String
  45. var sequencingCenter: String
    Definition Classes
    ReadGroupArgs
  46. var sortFastqOutput: Boolean
    Definition Classes
    SingleEndBwaMem2Args → ADAMSaveAnyArgs
  47. var stringency: String
  48. var sudo: Boolean
    Definition Classes
    BwaMem2Args
  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
    BwaMem2Args
  52. var useSingularity: Boolean
    Definition Classes
    BwaMem2Args
  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 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