Class

org.bdgenomics.cannoli.cli

BwaArgs

Related Doc: package cli

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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()

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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 addIndices: Boolean

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  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. var bwaPath: String

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  10. def clone(): AnyRef

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

  11. var compressionCodec: CompressionCodecName

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  12. var deferMerging: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

  13. var disableDictionaryEncoding: Boolean

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  14. var disableFastConcat: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

  15. var doPrintUsage: Boolean

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    Definition Classes
    Args4jBase

  16. var dockerCmd: String

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  17. var dockerImage: String

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

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    Definition Classes
    AnyRef

  19. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  20. def finalize(): Unit

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

  21. var forceLoadIfastq: Boolean

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  22. var forceLoadParquet: Boolean

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

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    Definition Classes
    AnyRef → Any

  24. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  25. var indexPath: String

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  26. var inputPath: String

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  27. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  28. var logLevel: String

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    Definition Classes
    ParquetArgs

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

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    Definition Classes
    AnyRef

  30. final def notify(): Unit

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    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  32. var outputPath: String

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    Definition Classes
    BwaArgs → SaveArgs

  33. var pageSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs

  34. var printMetrics: Boolean

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    Definition Classes
    Args4jBase

  35. var sample: String

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  36. var sequenceDictionary: String

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  37. var sortFastqOutput: Boolean

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    Definition Classes
    BwaArgs → ADAMSaveAnyArgs

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

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    Definition Classes
    AnyRef

  39. def toString(): String

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    Definition Classes
    AnyRef → Any

  40. var useDocker: Boolean

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  41. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  43. 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 Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped