Class

org.bdgenomics.cannoli.cli

BwaArgs

Related Doc: package cli

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class BwaArgs extends BwaFnArgs with ADAMSaveAnyArgs with ParquetArgs

Bwa command line arguments.

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

Instance Constructors

  1. new BwaArgs()

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Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. var addFiles: Boolean

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    Definition Classes
    BwaFnArgs
  5. var asFragments: Boolean

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  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  7. var asSingleFile: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs
  8. var blockSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  9. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  10. var compressionCodec: CompressionCodecName

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  11. var deferMerging: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs
  12. var disableDictionaryEncoding: Boolean

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  13. var disableFastConcat: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs
  14. var doPrintUsage: Boolean

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    Definition Classes
    Args4jBase
  15. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  17. var executable: String

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    Definition Classes
    BwaFnArgs
  18. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  19. var forceLoadIfastq: Boolean

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  20. var forceLoadParquet: Boolean

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

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    Definition Classes
    AnyRef → Any
  22. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  23. var image: String

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    Definition Classes
    BwaFnArgs
  24. var indexPath: String

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    Definition Classes
    BwaFnArgs
  25. var inputPath: String

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  26. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  27. var logLevel: String

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    Definition Classes
    ParquetArgs
  28. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  29. final def notify(): Unit

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    Definition Classes
    AnyRef
  30. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  31. var outputPath: String

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    Definition Classes
    BwaArgs → SaveArgs
  32. var pageSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  33. var printMetrics: Boolean

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    Definition Classes
    Args4jBase
  34. var sample: String

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    Definition Classes
    BwaFnArgs
  35. var sequenceDictionary: String

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  36. var sortFastqOutput: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs
  37. var stringency: String

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  38. var sudo: Boolean

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    Definition Classes
    BwaFnArgs
  39. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  40. def toString(): String

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    Definition Classes
    AnyRef → Any
  41. var useDocker: Boolean

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    Definition Classes
    BwaFnArgs
  42. var useSingularity: Boolean

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    Definition Classes
    BwaFnArgs
  43. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  44. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  45. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from BwaFnArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped