c

org.bdgenomics.cannoli.cli

SamtoolsMpileupArgs

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

Samtools mpileup command line arguments.

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

Instance Constructors

  1. new SamtoolsMpileupArgs()

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
    SamtoolsMpileupArgs
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. var asSingleFile: Boolean
    Definition Classes
    SamtoolsMpileupArgs → ADAMSaveAnyArgs
  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
    SamtoolsMpileupArgs → ADAMSaveAnyArgs
  13. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  14. var disableFastConcat: Boolean
    Definition Classes
    SamtoolsMpileupArgs → 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. var executable: String
    Definition Classes
    SamtoolsMpileupArgs
  19. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  20. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  21. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  22. var image: String
    Definition Classes
    SamtoolsMpileupArgs
  23. var inputPath: String
  24. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  25. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  26. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  28. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  29. var outputPath: String
    Definition Classes
    SamtoolsMpileupArgs → SaveArgs
  30. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  31. var referencePath: String
    Definition Classes
    SamtoolsMpileupArgs
  32. var sortFastqOutput: Boolean
    Definition Classes
    SamtoolsMpileupArgs → ADAMSaveAnyArgs
  33. var stringency: String
  34. var sudo: Boolean
    Definition Classes
    SamtoolsMpileupArgs
  35. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  36. def toString(): String
    Definition Classes
    AnyRef → Any
  37. var useDocker: Boolean
    Definition Classes
    SamtoolsMpileupArgs
  38. var useSingularity: Boolean
    Definition Classes
    SamtoolsMpileupArgs
  39. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  40. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  41. 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.SamtoolsMpileupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped