c

org.bdgenomics.cannoli.cli

BcftoolsMpileupArgs

class BcftoolsMpileupArgs extends cannoli.BcftoolsMpileupArgs with ADAMSaveAnyArgs with ParquetArgs

Bcftools mpileup command line arguments.

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

Instance Constructors

  1. new BcftoolsMpileupArgs()

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

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.BcftoolsMpileupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped