Class

nl.biopet.tools.vcfstats

Args

Related Doc: package vcfstats

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case class Args(inputFile: File = null, outputDir: File = null, referenceFile: File = null, intervals: Option[File] = None, infoTags: List[VcfField] = Nil, genotypeTags: List[VcfField] = Nil, binSize: Int = 10000000, maxContigsInSingleJob: Int = 250, writeBinStats: Boolean = false, localThreads: Int = 1, repartition: Boolean = false, executeModulesAsJobs: Boolean = false, notWriteContigStats: Boolean = false, sparkMaster: Option[String] = None, sparkConfigValues: Map[String, String] = ..., contigSampleOverlapPlots: Boolean = false, sampleToSampleMinDepth: Option[Int] = None, skipGeneral: Boolean = false, skipGenotype: Boolean = false, skipSampleDistributions: Boolean = false, skipSampleCompare: Boolean = false) extends Product with Serializable

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Instance Constructors

  1. new Args(inputFile: File = null, outputDir: File = null, referenceFile: File = null, intervals: Option[File] = None, infoTags: List[VcfField] = Nil, genotypeTags: List[VcfField] = Nil, binSize: Int = 10000000, maxContigsInSingleJob: Int = 250, writeBinStats: Boolean = false, localThreads: Int = 1, repartition: Boolean = false, executeModulesAsJobs: Boolean = false, notWriteContigStats: Boolean = false, sparkMaster: Option[String] = None, sparkConfigValues: Map[String, String] = ..., contigSampleOverlapPlots: Boolean = false, sampleToSampleMinDepth: Option[Int] = None, skipGeneral: Boolean = false, skipGenotype: Boolean = false, skipSampleDistributions: Boolean = false, skipSampleCompare: Boolean = false)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

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

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  4. final def asInstanceOf[T0]: T0

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  5. val binSize: Int

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  6. def clone(): AnyRef

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

  7. val contigSampleOverlapPlots: Boolean

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

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    Definition Classes
    AnyRef

  9. val executeModulesAsJobs: Boolean

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  10. def finalize(): Unit

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

  11. val genotypeTags: List[VcfField]

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

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    Definition Classes
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  13. val infoTags: List[VcfField]

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  14. val inputFile: File

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  15. val intervals: Option[File]

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  16. final def isInstanceOf[T0]: Boolean

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    Definition Classes
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  17. val localThreads: Int

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  18. val maxContigsInSingleJob: Int

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

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    Definition Classes
    AnyRef

  20. val notWriteContigStats: Boolean

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  21. final def notify(): Unit

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    Definition Classes
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  22. final def notifyAll(): Unit

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    Definition Classes
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  23. val outputDir: File

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  24. val referenceFile: File

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  25. val repartition: Boolean

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  26. val sampleToSampleMinDepth: Option[Int]

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  27. val skipGeneral: Boolean

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  28. val skipGenotype: Boolean

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  29. val skipSampleCompare: Boolean

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  30. val skipSampleDistributions: Boolean

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  31. val sparkConfigValues: Map[String, String]

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  32. val sparkMaster: Option[String]

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

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    Definition Classes
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  34. final def wait(): Unit

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    @throws( ... )

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

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

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    @throws( ... )

  37. val writeBinStats: Boolean

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Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

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Inherited from Any

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