Class

dagr.tasks.bwa

BwaSampe

Related Doc: package bwa

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class BwaSampe extends ProcessTask with FixedResources

Class for running "bwa sampe"

Linear Supertypes
FixedResources, ScheduleWithEmptyDefaultResources, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. BwaSampe
  2. FixedResources
  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 BwaSampe(r1Fastq: PathToFastq, r2Fastq: PathToFastq, r1Sai: FilePath, r2Sai: FilePath, out: PathToBam, ref: PathToFasta)

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

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

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

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    Definition Classes
    UnitTask → Schedulable

  14. def args: Seq[Any]

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    Definition Classes
    BwaSampe → ProcessTask

  15. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  16. def clone(): AnyRef

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

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

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

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

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

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

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

  20. def ensuring(cond: Boolean): BwaSampe

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

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    Definition Classes
    UnitTask → 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. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  30. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  31. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  33. final def notify(): Unit

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    Definition Classes
    AnyRef

  34. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  35. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  36. val out: PathToBam

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  37. def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    FixedResources → Schedulable

  38. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  39. val r1Fastq: PathToFastq

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  40. val r1Sai: FilePath

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  41. val r2Fastq: PathToFastq

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  42. val r2Sai: FilePath

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  43. val ref: PathToFasta

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  44. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  45. def requires(cores: Double, memory: String): BwaSampe.this.type

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    Definition Classes
    FixedResources

  46. def requires(cores: Cores, memory: Memory): BwaSampe.this.type

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    Definition Classes
    FixedResources

  47. def requires(resources: ResourceSet): BwaSampe.this.type

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    Definition Classes
    FixedResources

  48. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  50. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  51. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  52. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  53. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  54. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  57. def withName(name: String): BwaSampe.this.type

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    Definition Classes
    Task

  58. def →[B](y: B): (BwaSampe, B)

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

Inherited from FixedResources

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 BwaSampe to any2stringadd[BwaSampe]

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

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

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

Ungrouped