Class

org.bdgenomics.adam.cli

TransformFragmentsArgs

Related Doc: package cli

Permalink

class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

Instance Constructors

  1. new TransformFragmentsArgs()

    Permalink

Value Members

  1. final def !=(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

  5. var asSingleFile: Boolean

    Permalink
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  6. var binQualityScores: String

    Permalink

  7. var blockSize: Int

    Permalink
    Definition Classes
    ParquetArgs → ParquetRDDArgs

  8. def clone(): AnyRef

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  9. var compressionCodec: CompressionCodecName

    Permalink
    Definition Classes
    ParquetArgs → ParquetRDDArgs

  10. var deferMerging: Boolean

    Permalink
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  11. var disableDictionaryEncoding: Boolean

    Permalink
    Definition Classes
    ParquetArgs → ParquetRDDArgs

  12. var disableFastConcat: Boolean

    Permalink
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  13. var doPrintUsage: Boolean

    Permalink
    Definition Classes
    Args4jBase

  14. final def eq(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef

  15. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  16. def finalize(): Unit

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  17. final def getClass(): Class[_]

    Permalink
    Definition Classes
    AnyRef → Any

  18. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  19. var inputPath: String

    Permalink

  20. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  21. var loadAsReads: Boolean

    Permalink

  22. var logLevel: String

    Permalink
    Definition Classes
    ParquetArgs

  23. var markDuplicates: Boolean

    Permalink

  24. final def ne(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef

  25. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  26. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  27. var outputPath: String

    Permalink
    Definition Classes
    TransformFragmentsArgs → SaveArgs

  28. var pageSize: Int

    Permalink
    Definition Classes
    ParquetArgs → ParquetRDDArgs

  29. var printMetrics: Boolean

    Permalink
    Definition Classes
    Args4jBase

  30. var saveAsReads: Boolean

    Permalink

  31. var sortFastqOutput: Boolean

    Permalink
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs

  32. var sortLexicographically: Boolean

    Permalink

  33. var sortReads: Boolean

    Permalink

  34. final def synchronized[T0](arg0: ⇒ T0): T0

    Permalink
    Definition Classes
    AnyRef

  35. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  36. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  37. final def wait(arg0: Long, arg1: Int): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  38. final def wait(arg0: Long): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped