Class

dagr.tasks.picard

DeleteBam

Related Doc: package picard

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class DeleteBam extends SimpleInJvmTask

Class to remove a BAM file and also the BAI file if it exists. Succeeds if the files can be deleted, *or* if no files were present to be deleted.

Linear Supertypes
SimpleInJvmTask, FixedResources, ScheduleWithEmptyDefaultResources, InJvmTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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  2. By Inheritance
Inherited
  1. DeleteBam
  2. SimpleInJvmTask
  3. FixedResources
  4. ScheduleWithEmptyDefaultResources
  5. InJvmTask
  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 DeleteBam(bam: 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 DeleteBam to any2stringadd[DeleteBam] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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    Implicit information
    This member is added by an implicit conversion from DeleteBam to ArrowAssoc[DeleteBam] 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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  15. val bam: Path*

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  16. def clone(): AnyRef

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

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

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

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

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

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

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

  20. def ensuring(cond: Boolean): DeleteBam

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    Implicit information
    This member is added by an implicit conversion from DeleteBam to Ensuring[DeleteBam] 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 DeleteBam to StringFormat[DeleteBam] 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[_ <: DeleteBam.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. def inJvmMethod(): Int

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    Definition Classes
    SimpleInJvmTask → InJvmTask

  30. final def inJvmMethod(script: Path, logFile: Path): Int

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    Definition Classes
    InJvmTask

  31. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  32. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  33. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  35. final def notify(): Unit

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    Definition Classes
    AnyRef

  36. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  37. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    FixedResources → Schedulable

  39. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  40. def requires(cores: Double, memory: String): DeleteBam.this.type

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    Definition Classes
    FixedResources

  41. def requires(cores: Cores, memory: Memory): DeleteBam.this.type

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    Definition Classes
    FixedResources

  42. def requires(resources: ResourceSet): DeleteBam.this.type

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    Definition Classes
    FixedResources

  43. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

  44. def run(): Unit

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    Definition Classes
    DeleteBam → SimpleInJvmTask

  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
    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): DeleteBam.this.type

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    Definition Classes
    Task

  54. def →[B](y: B): (DeleteBam, B)

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

Inherited from SimpleInJvmTask

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from InJvmTask

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 DeleteBam to any2stringadd[DeleteBam]

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

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

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

Ungrouped