org.bdgenomics.cannoli.cli

BwaArgs

class BwaArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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Inherited
  1. BwaArgs
  2. ParquetArgs
  3. ADAMSaveAnyArgs
  4. SaveArgs
  5. ParquetRDDArgs
  6. Args4jBase
  7. AnyRef
  8. Any
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Visibility
  1. Public
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Instance Constructors

  1. new BwaArgs()

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. var addIndices: Boolean

  7. var asFragments: Boolean

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. var asSingleFile: Boolean

    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

  10. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  11. var bwaPath: String

  12. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  13. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  14. var deferMerging: Boolean

    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

  15. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  16. var disableFastConcat: Boolean

    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

  17. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase

  18. var dockerCmd: String

  19. var dockerImage: String

  20. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  21. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  22. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  23. var forceLoadIfastq: Boolean

  24. var forceLoadParquet: Boolean

  25. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  26. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  27. var indexPath: String

  28. var inputPath: String

  29. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  30. var logLevel: String

    Definition Classes
    ParquetArgs

  31. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  32. final def notify(): Unit

    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  34. var outputPath: String

    Definition Classes
    BwaArgs → SaveArgs

  35. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  36. var printMetrics: Boolean

    Definition Classes
    Args4jBase

  37. var sample: String

  38. var sequenceDictionary: String

  39. var sortFastqOutput: Boolean

    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

  40. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  41. def toString(): String

    Definition Classes
    AnyRef → Any

  42. var useDocker: Boolean

  43. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  44. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  45. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped