Class

org.bdgenomics.cannoli.cli

FreebayesArgs

Related Doc: package cli

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class FreebayesArgs extends FreebayesFnArgs with ADAMSaveAnyArgs with ParquetArgs

Freebayes command line arguments.

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

Instance Constructors

  1. new FreebayesArgs()

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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
    FreebayesFnArgs
  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  6. var asSingleFile: Boolean

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    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  7. var blockSize: Int

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

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

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  10. var deferMerging: Boolean

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    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  11. var disableDictionaryEncoding: Boolean

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  12. var disableFastConcat: Boolean

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    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  13. var doPrintUsage: Boolean

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

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

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    Definition Classes
    AnyRef → Any
  16. var executable: String

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    Definition Classes
    FreebayesFnArgs
  17. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  19. var gvcf: Boolean

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    Definition Classes
    FreebayesFnArgs
  20. var gvcfChunk: Int

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    Definition Classes
    FreebayesFnArgs
  21. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  22. var image: String

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    Definition Classes
    FreebayesFnArgs
  23. var inputPath: String

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  24. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  25. var logLevel: String

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

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

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

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    Definition Classes
    AnyRef
  29. var outputPath: String

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    Definition Classes
    FreebayesArgs → SaveArgs
  30. var pageSize: Int

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    Definition Classes
    ParquetArgs → ParquetRDDArgs
  31. var printMetrics: Boolean

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    Definition Classes
    Args4jBase
  32. var referencePath: String

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    Definition Classes
    FreebayesFnArgs
  33. var sortFastqOutput: Boolean

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    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  34. var stringency: String

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  35. var sudo: Boolean

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    Definition Classes
    FreebayesFnArgs
  36. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  37. def toString(): String

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    Definition Classes
    AnyRef → Any
  38. var useDocker: Boolean

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    Definition Classes
    FreebayesFnArgs
  39. var useSingularity: Boolean

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    Definition Classes
    FreebayesFnArgs
  40. final def wait(): Unit

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  42. 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 FreebayesFnArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped