Class/Object

dagr.pipelines

DnaResequencingFromUnmappedBamPipeline

Related Docs: object DnaResequencingFromUnmappedBamPipeline | package pipelines

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class DnaResequencingFromUnmappedBamPipeline extends Pipeline

Annotations
@ClpAnnotation()
Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. DnaResequencingFromUnmappedBamPipeline
  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 DnaResequencingFromUnmappedBamPipeline(unmappedBam: PathToBam, ref: PathToFasta, useBwaBacktrack: Boolean = false, downsampleToReads: Long = Math.round(185e6 / 101), targetIntervals: Option[PathToIntervals], tmp: Path, out: DirPath, basename: FilenamePrefix)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  3. def !=>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  4. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  5. def +(other: String): String

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

  6. def ->[B](y: B): (DnaResequencingFromUnmappedBamPipeline, B)

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

  7. def ::(other: Task): MultiTask

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef → Any

  9. def ==>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  10. def ==>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  11. def addTask(task: Task): task.type

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    Definition Classes
    Pipeline

  12. def addTasks(task: Task*): Unit

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    Definition Classes
    Pipeline

  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  14. val basename: FilenamePrefix

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  15. def build(): Unit

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    Definition Classes
    DnaResequencingFromUnmappedBamPipeline → Pipeline

  16. def clone(): AnyRef

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

  17. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  18. val downsampleToReads: Long

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

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

  20. def ensuring(cond: (DnaResequencingFromUnmappedBamPipeline) ⇒ Boolean): DnaResequencingFromUnmappedBamPipeline

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

  21. def ensuring(cond: Boolean, msg: ⇒ Any): DnaResequencingFromUnmappedBamPipeline

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

  22. def ensuring(cond: Boolean): DnaResequencingFromUnmappedBamPipeline

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

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

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    Definition Classes
    AnyRef

  24. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  25. def finalize(): Unit

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

  26. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    Pipeline → Task

  29. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  30. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  31. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  32. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  34. final def notify(): Unit

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    Definition Classes
    AnyRef

  35. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  36. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  37. val out: DirPath

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  38. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  39. val ref: PathToFasta

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  40. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  41. def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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    Definition Classes
    Task

  42. val root: Dependable

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    Definition Classes
    Pipeline

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

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    Definition Classes
    AnyRef

  44. val targetIntervals: Option[PathToIntervals]

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  45. val tmp: Path

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  46. def toString(): String

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    Definition Classes
    AnyRef → Any

  47. val unmappedBam: PathToBam

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  48. val useBwaBacktrack: Boolean

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  49. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  52. def withName(name: String): DnaResequencingFromUnmappedBamPipeline.this.type

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    Definition Classes
    Task

  53. def →[B](y: B): (DnaResequencingFromUnmappedBamPipeline, B)

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

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

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

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

Ungrouped