Class/Object

dagr.tasks.bwa

BwaK8AltProcessor

Related Docs: object BwaK8AltProcessor | package bwa

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class BwaK8AltProcessor extends ProcessTask with FixedResources with Configuration with Pipe[Sam, Sam]

Task for running the alt-mapping post-processing setup from bwa.kit. By default reads from stdin, but an input file can be supplied. Writes to stdout.

Linear Supertypes
Pipe[Sam, Sam], Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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  2. By Inheritance
Inherited
  1. BwaK8AltProcessor
  2. Pipe
  3. Configuration
  4. ConfigurationLike
  5. FixedResources
  6. ScheduleWithEmptyDefaultResources
  7. ProcessTask
  8. UnitTask
  9. Schedulable
  10. LazyLogging
  11. Task
  12. Dependable
  13. AnyRef
  14. 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 BwaK8AltProcessor(in: Option[Path] = None, altFile: Path)

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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 BwaK8AltProcessor to any2stringadd[BwaK8AltProcessor] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (BwaK8AltProcessor, B)

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to ArrowAssoc[BwaK8AltProcessor] 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[Sam, Void]

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    Definition Classes
    Pipe

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

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    Definition Classes
    Pipe

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

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    Definition Classes
    Pipe

  14. def >>!(path: Path): Pipe[Sam, 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
    UnitTask → Schedulable

  18. def args: Seq[Any]

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    Definition Classes
    BwaK8AltProcessor → ProcessTask

  19. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  20. def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  21. def clone(): AnyRef

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

  22. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  23. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

  24. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike

  25. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike

  26. def configureExecutable(path: String, executable: String): Path

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    Definition Classes
    ConfigurationLike

  27. def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

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    Definition Classes
    ConfigurationLike

  28. def discardError(): Pipe[Sam, Sam]

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    Definition Classes
    Pipe

  29. def ensuring(cond: (BwaK8AltProcessor) ⇒ Boolean, msg: ⇒ Any): BwaK8AltProcessor

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to Ensuring[BwaK8AltProcessor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  30. def ensuring(cond: (BwaK8AltProcessor) ⇒ Boolean): BwaK8AltProcessor

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to Ensuring[BwaK8AltProcessor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  31. def ensuring(cond: Boolean, msg: ⇒ Any): BwaK8AltProcessor

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to Ensuring[BwaK8AltProcessor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  32. def ensuring(cond: Boolean): BwaK8AltProcessor

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to Ensuring[BwaK8AltProcessor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  34. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  35. def finalize(): Unit

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

  36. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to StringFormat[BwaK8AltProcessor] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

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

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    Definition Classes
    AnyRef → Any

  38. final def getTasks: Traversable[_ <: BwaK8AltProcessor.this.type]

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    Definition Classes
    UnitTask → Task

  39. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  40. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  41. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  42. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  43. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  45. final def notify(): Unit

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    Definition Classes
    AnyRef

  46. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  47. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  48. def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    FixedResources → Schedulable

  50. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  51. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  52. def requires(cores: Double, memory: String): BwaK8AltProcessor.this.type

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    Definition Classes
    FixedResources

  53. def requires(cores: Cores, memory: Memory): BwaK8AltProcessor.this.type

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    Definition Classes
    FixedResources

  54. def requires(resources: ResourceSet): BwaK8AltProcessor.this.type

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    Definition Classes
    FixedResources

  55. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  57. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  58. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  59. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  60. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  61. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  62. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  65. def withName(name: String): BwaK8AltProcessor.this.type

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    Definition Classes
    Task

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

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    Definition Classes
    Pipe

  67. def →[B](y: B): (BwaK8AltProcessor, B)

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    Implicit information
    This member is added by an implicit conversion from BwaK8AltProcessor to ArrowAssoc[BwaK8AltProcessor] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Pipe[Sam, Sam]

Inherited from Configuration

Inherited from ConfigurationLike

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 BwaK8AltProcessor to any2stringadd[BwaK8AltProcessor]

Inherited by implicit conversion StringFormat from BwaK8AltProcessor to StringFormat[BwaK8AltProcessor]

Inherited by implicit conversion Ensuring from BwaK8AltProcessor to Ensuring[BwaK8AltProcessor]

Inherited by implicit conversion ArrowAssoc from BwaK8AltProcessor to ArrowAssoc[BwaK8AltProcessor]

Ungrouped