c

org.bdgenomics.cannoli.cli

BcftoolsCallArgs

class BcftoolsCallArgs extends cannoli.BcftoolsCallArgs with ADAMSaveAnyArgs with ParquetArgs

Bcftools call command line arguments.

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

Instance Constructors

  1. new BcftoolsCallArgs()

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
    BcftoolsCallArgs
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    BcftoolsCallArgs → ADAMSaveAnyArgs
  7. var bcftoolsArgs: String
    Definition Classes
    BcftoolsCallArgs
  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
    BcftoolsCallArgs → ADAMSaveAnyArgs
  12. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  13. var disableFastConcat: Boolean
    Definition Classes
    BcftoolsCallArgs → 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
    BcftoolsCallArgs
  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
    BcftoolsCallArgs
  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
    BcftoolsCallArgs → SaveArgs
  29. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  30. var sortFastqOutput: Boolean
    Definition Classes
    BcftoolsCallArgs → ADAMSaveAnyArgs
  31. var stringency: String
  32. var sudo: Boolean
    Definition Classes
    BcftoolsCallArgs
  33. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  34. def toString(): String
    Definition Classes
    AnyRef → Any
  35. var useDocker: Boolean
    Definition Classes
    BcftoolsCallArgs
  36. var useSingularity: Boolean
    Definition Classes
    BcftoolsCallArgs
  37. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  39. 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.BcftoolsCallArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped