Class

dagr.pipelines

DownsampleAndCallSomaticVariants

Related Doc: package pipelines

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class DownsampleAndCallSomaticVariants extends Pipeline

Pipeline to downsample a Tumor to a specific median coverage level (per CollectHsMetrics) and run somatic variant calling on it.

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. DownsampleAndCallSomaticVariants
  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 DownsampleAndCallSomaticVariants(tumorBam: PathToBam, normalBam: PathToBam, ref: PathToFasta, intervals: PathToIntervals, coverage: Seq[Int], output: DirPath)

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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 DownsampleAndCallSomaticVariants to any2stringadd[DownsampleAndCallSomaticVariants] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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    Implicit information
    This member is added by an implicit conversion from DownsampleAndCallSomaticVariants to ArrowAssoc[DownsampleAndCallSomaticVariants] 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
    DownsampleAndCallSomaticVariants → 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. val coverage: Seq[Int]

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  18. def ensuring(cond: (DownsampleAndCallSomaticVariants) ⇒ Boolean, msg: ⇒ Any): DownsampleAndCallSomaticVariants

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

  19. def ensuring(cond: (DownsampleAndCallSomaticVariants) ⇒ Boolean): DownsampleAndCallSomaticVariants

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

  20. def ensuring(cond: Boolean, msg: ⇒ Any): DownsampleAndCallSomaticVariants

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

  21. def ensuring(cond: Boolean): DownsampleAndCallSomaticVariants

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

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

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    Definition Classes
    AnyRef

  23. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  24. def finalize(): Unit

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

  25. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    Pipeline → Task

  28. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  29. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  30. val intervals: PathToIntervals

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  31. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  32. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  33. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  35. val normalBam: PathToBam

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  36. final def notify(): Unit

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    Definition Classes
    AnyRef

  37. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  38. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  39. val output: DirPath

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  40. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  41. def pad(i: Int): String

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    Pads out a coverage number to a 3-digit String, and adds X on the end.

  42. val ref: PathToFasta

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  43. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  44. val root: Dependable

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    Definition Classes
    Pipeline

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

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    Definition Classes
    AnyRef

  46. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  47. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  48. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  49. def toString(): String

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    Definition Classes
    AnyRef → Any

  50. val tumorBam: PathToBam

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  51. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  54. def withName(name: String): DownsampleAndCallSomaticVariants.this.type

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    Definition Classes
    Task

  55. def →[B](y: B): (DownsampleAndCallSomaticVariants, B)

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    Implicit information
    This member is added by an implicit conversion from DownsampleAndCallSomaticVariants to ArrowAssoc[DownsampleAndCallSomaticVariants] 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 DownsampleAndCallSomaticVariants to any2stringadd[DownsampleAndCallSomaticVariants]

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

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

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

Ungrouped