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: Dependable): Dependable

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    Definition Classes
    Dependable
  7. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  8. final def ==>(other: Dependable): Dependable

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    Definition Classes
    Dependable
  9. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable
  10. def addSubcommandArgs(buffer: ListBuffer[Any]): Unit

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    Definition Classes
    SamtoolsFaidxSamtoolsTask
  11. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable
  12. def args: Seq[Any]

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    Definition Classes
    SamtoolsTask → ProcessTask
  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  14. def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  15. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  16. val command: String

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    Definition Classes
    SamtoolsTask
  17. def commandLineName: String

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    Definition Classes
    ConfigurationLike
  18. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike
  19. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  20. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  21. def configureExecutable(path: String, executable: String): Path

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    Definition Classes
    ConfigurationLike
  22. def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

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    Definition Classes
    ConfigurationLike
  23. 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
  24. 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
  25. 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
  26. 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
  27. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  28. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  29. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  30. 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()
  31. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  32. final def getTasks: Traversable[_ <: SamtoolsFaidx.this.type]

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    Definition Classes
    UnitTask → Task
  33. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  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 optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

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    Definition Classes
    ConfigurationLike
  42. def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    FixedResources → Schedulable
  43. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask
  44. val ref: PathToFasta

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  45. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task
  46. def requires(cores: Double, memory: String): SamtoolsFaidx.this.type

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    Definition Classes
    FixedResources
  47. def requires(cores: Cores, memory: Memory): SamtoolsFaidx.this.type

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    Definition Classes
    FixedResources
  48. def requires(resources: ResourceSet): SamtoolsFaidx.this.type

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    Definition Classes
    FixedResources
  49. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources
  50. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  51. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  52. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task
  53. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task
  54. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any
  55. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  56. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  57. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  58. def withName(name: String): SamtoolsFaidx.this.type

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    Definition Classes
    Task
  59. 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