Class

dagr.pipelines

SomaticVariantCallingPipeline

Related Doc: package pipelines

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class SomaticVariantCallingPipeline extends Pipeline

Pipeline to call Somatic Variants using both Varscan2 and Mutect2

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. SomaticVariantCallingPipeline
  2. Pipeline
  3. LazyLogging
  4. Task
  5. Dependable
  6. AnyRef
  7. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new SomaticVariantCallingPipeline(tumorBam: PathToBam, normalBam: PathToBam, ref: PathToFasta, intervals: PathToIntervals, outputPrefix: DirPath, includeMutect2: Boolean = false, includeFreeBayes: Boolean = false, removeIntermediates: Boolean = false)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: Dependable): Unit

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    Definition Classes
    Task → Dependable

  3. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  4. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to any2stringadd[SomaticVariantCallingPipeline] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (SomaticVariantCallingPipeline, B)

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to ArrowAssoc[SomaticVariantCallingPipeline] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

  6. def ::(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable

  7. def ::(other: Dependable): Dependable

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    Definition Classes
    Dependable

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

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    Definition Classes
    AnyRef → Any

  9. final def ==>(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable

  10. final def ==>(other: Dependable): Dependable

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    Definition Classes
    Dependable

  11. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable

  12. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  14. def build(): Unit

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    Definition Classes
    SomaticVariantCallingPipeline → Pipeline

  15. def clone(): AnyRef

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

  16. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  17. def ensuring(cond: (SomaticVariantCallingPipeline) ⇒ Boolean, msg: ⇒ Any): SomaticVariantCallingPipeline

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to Ensuring[SomaticVariantCallingPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  18. def ensuring(cond: (SomaticVariantCallingPipeline) ⇒ Boolean): SomaticVariantCallingPipeline

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to Ensuring[SomaticVariantCallingPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  19. def ensuring(cond: Boolean, msg: ⇒ Any): SomaticVariantCallingPipeline

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to Ensuring[SomaticVariantCallingPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  20. def ensuring(cond: Boolean): SomaticVariantCallingPipeline

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to Ensuring[SomaticVariantCallingPipeline] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  22. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  23. def finalize(): Unit

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

  24. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to StringFormat[SomaticVariantCallingPipeline] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

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

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    Definition Classes
    AnyRef → Any

  26. final def getTasks: Traversable[_ <: Task]

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    Definition Classes
    Pipeline → Task

  27. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  28. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  29. val includeFreeBayes: Boolean

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  30. val includeMutect2: Boolean

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  31. val intervals: PathToIntervals

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  32. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  33. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  34. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  36. val normalBam: PathToBam

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  37. final def notify(): Unit

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    Definition Classes
    AnyRef

  38. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  39. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  40. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  41. val outputPrefix: DirPath

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  42. val ref: PathToFasta

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  43. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  44. val removeIntermediates: Boolean

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  45. val root: Dependable

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    Definition Classes
    Pipeline

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

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    Definition Classes
    AnyRef

  47. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  48. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  49. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  50. def toString(): String

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    Definition Classes
    AnyRef → Any

  51. val tumorBam: PathToBam

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  52. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  55. def withName(name: String): SomaticVariantCallingPipeline.this.type

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    Definition Classes
    Task

  56. def →[B](y: B): (SomaticVariantCallingPipeline, B)

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    Implicit information
    This member is added by an implicit conversion from SomaticVariantCallingPipeline to ArrowAssoc[SomaticVariantCallingPipeline] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Pipeline

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from SomaticVariantCallingPipeline to any2stringadd[SomaticVariantCallingPipeline]

Inherited by implicit conversion StringFormat from SomaticVariantCallingPipeline to StringFormat[SomaticVariantCallingPipeline]

Inherited by implicit conversion Ensuring from SomaticVariantCallingPipeline to Ensuring[SomaticVariantCallingPipeline]

Inherited by implicit conversion ArrowAssoc from SomaticVariantCallingPipeline to ArrowAssoc[SomaticVariantCallingPipeline]

Ungrouped