Class

dagr.tasks.bwa

BwaMem

Related Doc: package bwa

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class BwaMem extends ProcessTask with VariableResources with Pipe[Fastq, Sam]

Linear Supertypes
Pipe[Fastq, Sam], VariableResources, ScheduleWithEmptyDefaultResources, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. BwaMem
  2. Pipe
  3. VariableResources
  4. ScheduleWithEmptyDefaultResources
  5. ProcessTask
  6. UnitTask
  7. Schedulable
  8. LazyLogging
  9. Task
  10. Dependable
  11. AnyRef
  12. 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 BwaMem(fastq: PathToFastq = Io.StdIn, out: Option[PathToBam] = None, ref: PathToFasta, minSeedLength: Option[Int] = None, matchScore: Option[Int] = None, mismatchPenalty: Option[Int] = None, gapOpenPenalties: Option[(Int, Int)] = None, gapExtensionPenalties: Option[(Int, Int)] = None, clippingPenalties: Option[(Int, Int)] = None, minScore: Option[Int] = None, smartPairing: Boolean = true, minThreads: Int = 1, maxThreads: Int = 32, memory: Memory = Memory("8G"))

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

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

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    Implicit information
    This member is added by an implicit conversion from BwaMem to ArrowAssoc[BwaMem] 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 >(path: Path): Pipe[Fastq, Void]

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    Definition Classes
    Pipe

  12. def >!(path: Path): Pipe[Fastq, Sam]

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    Definition Classes
    Pipe

  13. def >>(path: Path): Pipe[Fastq, Void]

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    Definition Classes
    Pipe

  14. def >>!(path: Path): Pipe[Fastq, Sam]

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    Definition Classes
    Pipe

  15. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable

  16. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  17. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    VariableResources → Schedulable

  18. def args: Seq[Any]

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    Definition Classes
    BwaMem → ProcessTask

  19. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  20. def clone(): AnyRef

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

  21. def discardError(): Pipe[Fastq, Sam]

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    Definition Classes
    Pipe

  22. def ensuring(cond: (BwaMem) ⇒ Boolean, msg: ⇒ Any): BwaMem

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

  23. def ensuring(cond: (BwaMem) ⇒ Boolean): BwaMem

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

  24. def ensuring(cond: Boolean, msg: ⇒ Any): BwaMem

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

  25. def ensuring(cond: Boolean): BwaMem

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

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

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    Definition Classes
    AnyRef

  27. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  28. def finalize(): Unit

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

  29. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  31. final def getTasks: Traversable[_ <: BwaMem.this.type]

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    Definition Classes
    UnitTask → Task

  32. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  33. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  34. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  35. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  36. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  38. final def notify(): Unit

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    Definition Classes
    AnyRef

  39. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  40. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    BwaMem → Schedulable

  42. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  43. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  44. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  46. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  47. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  48. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  49. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  50. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  53. def withName(name: String): BwaMem.this.type

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    Definition Classes
    Task

  54. def |[In2 >: Sam, Out2](next: Pipe[In2, Out2]): Pipe[Fastq, Out2]

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    Definition Classes
    Pipe

  55. def →[B](y: B): (BwaMem, B)

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

Inherited from Pipe[Fastq, Sam]

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 BwaMem to any2stringadd[BwaMem]

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

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

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

Ungrouped