c

org.bdgenomics.adam.cli

TransformFragmentsArgs

class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs with CramArgs

Linear Supertypes
CramArgs, ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. TransformFragmentsArgs
  2. CramArgs
  3. ParquetArgs
  4. ADAMSaveAnyArgs
  5. SaveArgs
  6. ParquetRDDArgs
  7. Args4jBase
  8. AnyRef
  9. 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[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
    TransformFragmentsArgs → ADAMSaveAnyArgs
  13. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  14. var disableFastConcat: Boolean
    Definition Classes
    TransformFragmentsArgs → 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. 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 inputPath: String
  22. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  23. var loadAsAlignments: Boolean
  24. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  25. var markDuplicates: Boolean
  26. var maxReadLength: Int
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  29. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  30. var outputPath: String
    Definition Classes
    TransformFragmentsArgs → SaveArgs
  31. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  32. var pairedFastqFile: String
  33. var saveAsAlignments: Boolean
  34. var sortByReadName: Boolean
  35. var sortByReferencePosition: Boolean
  36. var sortByReferencePositionAndIndex: Boolean
  37. var sortFastqOutput: Boolean
    Definition Classes
    TransformFragmentsArgs → ADAMSaveAnyArgs
  38. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  39. def toString(): String
    Definition Classes
    AnyRef → Any
  40. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  41. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  42. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()

Inherited from CramArgs

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped