Class

dagr.tasks.bwa

BwaAln

Related Doc: package bwa

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class BwaAln extends ProcessTask with VariableResources

Class for running "bwa aln"

Linear Supertypes
VariableResources, ScheduleWithEmptyDefaultResources, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. BwaAln
  2. VariableResources
  3. ScheduleWithEmptyDefaultResources
  4. ProcessTask
  5. UnitTask
  6. Schedulable
  7. LazyLogging
  8. Task
  9. Dependable
  10. AnyRef
  11. 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 BwaAln(in: PathToFastq, out: FilePath, ref: PathToFasta, maxCores: Int = 8)

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

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

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    Implicit information
    This member is added by an implicit conversion from BwaAln to ArrowAssoc[BwaAln] 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 applyResources(resources: ResourceSet): Unit

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    Definition Classes
    VariableResources → Schedulable

  12. def args: Seq[Any]

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    Definition Classes
    BwaAln → ProcessTask

  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  14. def clone(): AnyRef

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

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

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

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

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

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

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

  18. def ensuring(cond: Boolean): BwaAln

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    Implicit information
    This member is added by an implicit conversion from BwaAln to Ensuring[BwaAln] 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 BwaAln to StringFormat[BwaAln] 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[_ <: BwaAln.this.type]

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    Definition Classes
    UnitTask → Task

  25. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  26. val in: PathToFastq

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  27. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  28. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  29. val maxCores: Int

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  30. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  32. final def notify(): Unit

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    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  34. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  35. val out: FilePath

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  36. def pickResources(resources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    BwaAln → Schedulable

  37. val ref: PathToFasta

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  38. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  39. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  42. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  43. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  46. def withName(name: String): BwaAln.this.type

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    Definition Classes
    Task

  47. def →[B](y: B): (BwaAln, B)

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

Inherited from VariableResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from ProcessTask

Inherited from UnitTask

Inherited from Schedulable

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped