Class

dagr.tasks.samtools

SamtoolsTask

Related Doc: package samtools

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abstract class SamtoolsTask extends ProcessTask with Configuration

Base class for all tasks that run samtools.

Linear Supertypes
Configuration, ConfigurationLike, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
Known Subclasses
SamtoolsFaidx, SamtoolsPileup
Ordering
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  2. By Inheritance
Inherited
  1. SamtoolsTask
  2. Configuration
  3. ConfigurationLike
  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 SamtoolsTask(command: String)

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Abstract Value Members

  1. abstract def addSubcommandArgs(buffer: ListBuffer[Any]): Unit

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  2. abstract def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    Schedulable

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

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

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    Implicit information
    This member is added by an implicit conversion from SamtoolsTask to ArrowAssoc[SamtoolsTask] 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
    SamtoolsTask → ProcessTask

  15. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  17. def clone(): AnyRef

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

  18. val command: String

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  19. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  20. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  25. def ensuring(cond: (SamtoolsTask) ⇒ Boolean, msg: ⇒ Any): SamtoolsTask

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

  26. def ensuring(cond: (SamtoolsTask) ⇒ Boolean): SamtoolsTask

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

  27. def ensuring(cond: Boolean, msg: ⇒ Any): SamtoolsTask

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

  28. def ensuring(cond: Boolean): SamtoolsTask

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

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

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    Definition Classes
    AnyRef

  30. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  31. def finalize(): Unit

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

  32. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  34. final def getTasks: Traversable[_ <: SamtoolsTask.this.type]

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    Definition Classes
    UnitTask → Task

  35. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  36. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  37. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  38. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  39. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  41. final def notify(): Unit

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    Definition Classes
    AnyRef

  42. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  43. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

  45. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  46. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  48. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  49. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  50. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  51. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  52. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  53. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  56. def withName(name: String): SamtoolsTask.this.type

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    Definition Classes
    Task

  57. def →[B](y: B): (SamtoolsTask, B)

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

Inherited from Configuration

Inherited from ConfigurationLike

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 SamtoolsTask to any2stringadd[SamtoolsTask]

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

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

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

Ungrouped