c

org.bdgenomics.cannoli.cli

SingleEndBowtie2Args

class SingleEndBowtie2Args extends cannoli.SingleEndBowtie2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

Single-end read Bowtie 2 command line arguments.

Linear Supertypes
ParquetArgs, CramArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.SingleEndBowtie2Args, Args4jBase, AnyRef, Any
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Inherited
  1. SingleEndBowtie2Args
  2. ParquetArgs
  3. CramArgs
  4. ADAMSaveAnyArgs
  5. SaveArgs
  6. ParquetRDDArgs
  7. SingleEndBowtie2Args
  8. Args4jBase
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new SingleEndBowtie2Args()

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
    SingleEndBowtie2Args
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    SingleEndBowtie2Args → ADAMSaveAnyArgs
  7. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  8. var bowtie2Args: String
    Definition Classes
    SingleEndBowtie2Args
  9. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  10. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  11. def configureCramFormat(sc: SparkContext): Option[Unit]

    Configure CRAM format.

    Configure CRAM format.

    sc

    Spark context to configure

    Definition Classes
    CramArgs
  12. val cramReference: String
    Definition Classes
    CramArgs
    Annotations
    @Option()
  13. var deferMerging: Boolean
    Definition Classes
    SingleEndBowtie2Args → ADAMSaveAnyArgs
  14. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  15. var disableFastConcat: Boolean
    Definition Classes
    SingleEndBowtie2Args → ADAMSaveAnyArgs
  16. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  17. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  18. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  19. var executable: String
    Definition Classes
    SingleEndBowtie2Args
  20. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  21. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  22. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  23. var image: String
    Definition Classes
    SingleEndBowtie2Args
  24. var indexPath: String
    Definition Classes
    SingleEndBowtie2Args
  25. var inputPath: String
  26. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  27. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  28. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  29. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  30. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  31. var outputPath: String
    Definition Classes
    SingleEndBowtie2Args → SaveArgs
  32. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  33. var sortFastqOutput: Boolean
    Definition Classes
    SingleEndBowtie2Args → ADAMSaveAnyArgs
  34. var stringency: String
  35. var sudo: Boolean
    Definition Classes
    SingleEndBowtie2Args
  36. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  37. def toString(): String
    Definition Classes
    AnyRef → Any
  38. var useDocker: Boolean
    Definition Classes
    SingleEndBowtie2Args
  39. var useSingularity: Boolean
    Definition Classes
    SingleEndBowtie2Args
  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 ParquetArgs

Inherited from CramArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from cannoli.SingleEndBowtie2Args

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

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