Class

dagr.tasks.samtools

SamtoolsFaidx

Related Doc: package samtools

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class SamtoolsFaidx extends SamtoolsTask with FixedResources

Runs samtools faidx to create an index file for a fasta file

Linear Supertypes
FixedResources, ScheduleWithEmptyDefaultResources, SamtoolsTask, Configuration, ConfigurationLike, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. SamtoolsFaidx
  2. FixedResources
  3. ScheduleWithEmptyDefaultResources
  4. SamtoolsTask
  5. Configuration
  6. ConfigurationLike
  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 SamtoolsFaidx(ref: PathToFasta)

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

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

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    Implicit information
    This member is added by an implicit conversion from SamtoolsFaidx to ArrowAssoc[SamtoolsFaidx] 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 addSubcommandArgs(buffer: ListBuffer[Any]): Unit

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    Definition Classes
    SamtoolsFaidx → SamtoolsTask

  13. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  14. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable

  15. def args: Seq[Any]

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    Definition Classes
    SamtoolsTask → ProcessTask

  16. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  18. def clone(): AnyRef

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

  19. val command: String

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    Definition Classes
    SamtoolsTask

  20. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  21. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  26. def ensuring(cond: (SamtoolsFaidx) ⇒ Boolean, msg: ⇒ Any): SamtoolsFaidx

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

  27. def ensuring(cond: (SamtoolsFaidx) ⇒ Boolean): SamtoolsFaidx

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

  28. def ensuring(cond: Boolean, msg: ⇒ Any): SamtoolsFaidx

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

  29. def ensuring(cond: Boolean): SamtoolsFaidx

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

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

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    Definition Classes
    AnyRef

  31. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  32. def finalize(): Unit

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

  33. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  35. final def getTasks: Traversable[_ <: SamtoolsFaidx.this.type]

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    Definition Classes
    UnitTask → Task

  36. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  37. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  38. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  39. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  40. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  42. final def notify(): Unit

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    Definition Classes
    AnyRef

  43. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  44. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    FixedResources → Schedulable

  47. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  48. val ref: PathToFasta

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  49. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  50. def requires(cores: Double, memory: String): SamtoolsFaidx.this.type

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    Definition Classes
    FixedResources

  51. def requires(cores: Cores, memory: Memory): SamtoolsFaidx.this.type

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    Definition Classes
    FixedResources

  52. def requires(resources: ResourceSet): SamtoolsFaidx.this.type

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    Definition Classes
    FixedResources

  53. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  55. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  56. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  57. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  58. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  59. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  60. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  63. def withName(name: String): SamtoolsFaidx.this.type

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    Definition Classes
    Task

  64. def →[B](y: B): (SamtoolsFaidx, B)

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

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from SamtoolsTask

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 SamtoolsFaidx to any2stringadd[SamtoolsFaidx]

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

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

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

Ungrouped