c

org.bdgenomics.adam.cli

TransformFragmentsArgs

class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

Instance Constructors

  1. new TransformFragmentsArgs()

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. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. var asSingleFile: Boolean
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs
  6. var binQualityScores: String
  7. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  8. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  9. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  10. var deferMerging: Boolean
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs
  11. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  12. var disableFastConcat: Boolean
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs
  13. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  14. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  16. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  18. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  19. var inputPath: String
  20. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  21. var loadAsReads: Boolean
  22. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  23. var markDuplicates: Boolean
  24. var maxReadLength: Int
  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
    TransformFragmentsArgs → SaveArgs
  29. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  30. var printMetrics: Boolean
    Definition Classes
    Args4jBase
  31. var saveAsReads: Boolean
  32. var sortFastqOutput: Boolean
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs
  33. var sortLexicographically: Boolean
  34. var sortReads: Boolean
  35. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  36. def toString(): String
    Definition Classes
    AnyRef → Any
  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
    @native() @throws( ... )

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped