c

org.bdgenomics.cannoli.cli

SampleReadsArgs

class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Linear Supertypes
ParquetArgs, CramArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SampleReadsArgs
  2. ParquetArgs
  3. CramArgs
  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 SampleReadsArgs()

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
    SampleReadsArgs → ADAMSaveAnyArgs
  6. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  7. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  8. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  9. def configureCramFormat(sc: SparkContext): Option[Unit]

    Configure CRAM format.

    Configure CRAM format.

    sc

    Spark context to configure

    Definition Classes
    CramArgs
  10. val cramReference: String
    Definition Classes
    CramArgs
    Annotations
    @Option()
  11. var deferMerging: Boolean
    Definition Classes
    SampleReadsArgs → ADAMSaveAnyArgs
  12. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  13. var disableFastConcat: Boolean
    Definition Classes
    SampleReadsArgs → 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 fraction: Double
  18. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  19. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  20. var inputPath: String
  21. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  22. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  23. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  25. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  26. var outputPath: String
    Definition Classes
    SampleReadsArgs → SaveArgs
  27. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  28. var seed: Long
  29. var sortFastqOutput: Boolean
    Definition Classes
    SampleReadsArgs → ADAMSaveAnyArgs
  30. var stringency: String
  31. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  32. def toString(): String
    Definition Classes
    AnyRef → Any
  33. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  35. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from ParquetArgs

Inherited from CramArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped