c

org.bdgenomics.cannoli.cli

FreebayesArgs

class FreebayesArgs extends cannoli.FreebayesArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Freebayes command line arguments.

Linear Supertypes
ParquetArgs, CramArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.FreebayesArgs, Args4jBase, AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. FreebayesArgs
  2. ParquetArgs
  3. CramArgs
  4. ADAMSaveAnyArgs
  5. SaveArgs
  6. ParquetRDDArgs
  7. FreebayesArgs
  8. Args4jBase
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new FreebayesArgs()

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
    FreebayesArgs
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    FreebayesArgs → 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. var deferMerging: Boolean
    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  13. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  14. var disableFastConcat: Boolean
    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  15. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  16. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  18. var executable: String
    Definition Classes
    FreebayesArgs
  19. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  20. var freebayesArgs: String
    Definition Classes
    FreebayesArgs
  21. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  22. var gvcf: Boolean
    Definition Classes
    FreebayesArgs
  23. var gvcfChunk: Int
    Definition Classes
    FreebayesArgs
  24. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  25. var image: String
    Definition Classes
    FreebayesArgs
  26. var inputPath: String
  27. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  28. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  29. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  30. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  31. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  32. var outputPath: String
    Definition Classes
    FreebayesArgs → SaveArgs
  33. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  34. var referencePath: String
    Definition Classes
    FreebayesArgs
  35. var sortFastqOutput: Boolean
    Definition Classes
    FreebayesArgs → ADAMSaveAnyArgs
  36. var stringency: String
  37. var sudo: Boolean
    Definition Classes
    FreebayesArgs
  38. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  39. def toString(): String
    Definition Classes
    AnyRef → Any
  40. var useDocker: Boolean
    Definition Classes
    FreebayesArgs
  41. var useSingularity: Boolean
    Definition Classes
    FreebayesArgs
  42. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  43. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  44. 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.FreebayesArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped