Class

dagr.tasks.bwa

BwaSampe

Related Doc: package bwa

Permalink

class BwaSampe extends ProcessTask with FixedResources

Class for running "bwa sampe"

Linear Supertypes
FixedResources, ScheduleWithEmptyDefaultResources, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
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
  1. Hide All
  2. Show all
Visibility
  1. Public
  2. All

Instance Constructors

  1. new BwaSampe(r1Fastq: PathToFastq, r2Fastq: PathToFastq, r1Sai: FilePath, r2Sai: FilePath, out: PathToBam, ref: PathToFasta)

    Permalink

Value Members

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

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    Task → Dependable

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

    Permalink
    Definition Classes
    Task → Dependable

  4. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  5. def +(other: String): String

    Permalink
    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

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

    Permalink
    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()

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

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    Task → Dependable

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

    Permalink
    Definition Classes
    Task → Dependable

  11. def applyResources(resources: ResourceSet): Unit

    Permalink
    Definition Classes
    UnitTask → Schedulable

  12. def args: Seq[Any]

    Permalink
    Definition Classes
    BwaSampe → ProcessTask

  13. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

  14. def clone(): AnyRef

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

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

    Permalink
    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

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

    Permalink
    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

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

    Permalink
    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: Boolean): BwaSampe

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

    Permalink
    Definition Classes
    AnyRef

  20. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  21. def finalize(): Unit

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

  22. def formatted(fmtstr: String): String

    Permalink
    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()

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

    Permalink
    Definition Classes
    AnyRef → Any

  24. final def getTasks: Traversable[_ <: BwaSampe.this.type]

    Permalink
    Definition Classes
    UnitTask → Task

  25. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  26. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  27. lazy val logger: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    LazyLogging

  28. var name: String

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    AnyRef

  30. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  32. def onComplete(exitCode: Int): Boolean

    Permalink
    Definition Classes
    Task

  33. val out: PathToBam

    Permalink

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

    Permalink
    Definition Classes
    FixedResources → Schedulable

  35. val r1Fastq: PathToFastq

    Permalink

  36. val r1Sai: FilePath

    Permalink

  37. val r2Fastq: PathToFastq

    Permalink

  38. val r2Sai: FilePath

    Permalink

  39. val ref: PathToFasta

    Permalink

  40. def removeDependency(task: Task): Boolean

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    FixedResources

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

    Permalink
    Definition Classes
    FixedResources

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

    Permalink
    Definition Classes
    FixedResources

  44. def resources: ResourceSet

    Permalink
    Definition Classes
    ScheduleWithEmptyDefaultResources

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

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    AnyRef

  47. def toString(): String

    Permalink
    Definition Classes
    ProcessTask → AnyRef → Any

  48. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    Task

  52. def →[B](y: B): (BwaSampe, B)

    Permalink
    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