Class/Object

dagr.tasks.gatk

IndelRealignment

Related Docs: object IndelRealignment | package gatk

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class IndelRealignment extends Pipeline

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. IndelRealignment
  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 IndelRealignment(in: Seq[PathToBam], out: DirPath, ref: PathToFasta, known: Seq[PathToVcf] = Nil, intervals: Option[PathToIntervals] = None)

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    CLP constructor for testing and manual use, since there's no easy way to provide a map on the CLI.

  2. new IndelRealignment(bams: Map[PathToBam, PathToBam], ref: PathToFasta, known: Seq[PathToVcf], intervals: Option[PathToIntervals], bamCompression: Option[Int])

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

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

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

  6. def ::(other: Dependable): Dependable

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    Definition Classes
    Dependable

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

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    Dependable

  9. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable

  10. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  11. val bams: Map[PathToBam, PathToBam]

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  12. def build(): Unit

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    Constructs a mini pipeline that runs RealignerTargetCreator and IndelRealigner on multiple samples together.

    Constructs a mini pipeline that runs RealignerTargetCreator and IndelRealigner on multiple samples together.

    Definition Classes
    IndelRealignment → Pipeline

  13. def clone(): AnyRef

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

  14. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  15. def ensuring(cond: (IndelRealignment) ⇒ Boolean, msg: ⇒ Any): IndelRealignment

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

  16. def ensuring(cond: (IndelRealignment) ⇒ Boolean): IndelRealignment

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

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

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

  18. def ensuring(cond: Boolean): IndelRealignment

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

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

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    Definition Classes
    AnyRef

  20. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  21. def finalize(): Unit

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

  22. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    Pipeline → Task

  25. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  26. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  27. val known: Seq[PathToVcf]

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  28. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  29. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  31. final def notify(): Unit

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    Definition Classes
    AnyRef

  32. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  33. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  34. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  35. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  36. val root: Dependable

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    Definition Classes
    Pipeline

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

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    Definition Classes
    AnyRef

  38. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  39. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  40. def toString(): String

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    Definition Classes
    AnyRef → Any

  41. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  44. def withName(name: String): IndelRealignment.this.type

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    Definition Classes
    Task

  45. def →[B](y: B): (IndelRealignment, B)

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

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

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

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

Ungrouped