Class

dagr.tasks.vc

FreeBayesParallel

Related Doc: package vc

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class FreeBayesParallel extends ProcessTask with Configuration with VariableResources with Pipe[Text, Vcf]

Task to run freepayes using GNP parallel. This assumes regions are being piped into this task via a pipe chain.

Linear Supertypes
Pipe[Text, Vcf], VariableResources, ScheduleWithEmptyDefaultResources, Configuration, ConfigurationLike, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. FreeBayesParallel
  2. Pipe
  3. VariableResources
  4. ScheduleWithEmptyDefaultResources
  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 FreeBayesParallel(ref: PathToFasta, bam: List[PathToBam], somatic: Boolean, memory: Memory, minThreads: Int, maxThreads: Int, useBestNAlleles: Option[Int], maxCoverage: Option[Int], minRepeatEntropy: Option[Int], minAlternateAlleleFraction: Option[Float] = None)

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

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

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

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    Definition Classes
    Pipe

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

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    Definition Classes
    Pipe

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

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    Definition Classes
    Pipe

  14. def >>!(path: Path): Pipe[Text, Vcf]

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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
    VariableResources → Schedulable

  18. def args: Seq[Any]

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    Definition Classes
    FreeBayesParallel → 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. val bam: List[PathToBam]

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  22. def clone(): AnyRef

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

  23. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  24. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  29. def discardError(): Pipe[Text, Vcf]

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    Definition Classes
    Pipe

  30. def ensuring(cond: (FreeBayesParallel) ⇒ Boolean, msg: ⇒ Any): FreeBayesParallel

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

  31. def ensuring(cond: (FreeBayesParallel) ⇒ Boolean): FreeBayesParallel

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

  32. def ensuring(cond: Boolean, msg: ⇒ Any): FreeBayesParallel

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

  33. def ensuring(cond: Boolean): FreeBayesParallel

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

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

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    Definition Classes
    AnyRef

  35. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  36. def finalize(): Unit

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

  37. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  39. final def getTasks: Traversable[_ <: FreeBayesParallel.this.type]

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    Definition Classes
    UnitTask → Task

  40. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  41. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  42. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  43. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  44. val maxCoverage: Option[Int]

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  45. val maxThreads: Int

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  46. val memory: Memory

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  47. val minAlternateAlleleFraction: Option[Float]

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  48. val minRepeatEntropy: Option[Int]

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  49. val minThreads: Int

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  50. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  52. final def notify(): Unit

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    Definition Classes
    AnyRef

  53. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  54. def numThreads: Int

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    Attributes
    protected

  55. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

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

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    Attempts to pick the resources required to run.

    Attempts to pick the resources required to run. The required resources are: 1) Cores = the cores for freebayes plus one additional core to account for the other scripts 2) Memory = a fixed amount.

    Definition Classes
    FreeBayesParallel → Schedulable

  58. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  59. val ref: PathToFasta

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  60. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  61. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

  62. val somatic: Boolean

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

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    Definition Classes
    AnyRef

  64. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  65. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  66. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  67. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  68. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  69. val useBestNAlleles: Option[Int]

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  70. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  73. def withName(name: String): FreeBayesParallel.this.type

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    Definition Classes
    Task

  74. def |[In2 >: Vcf, Out2](next: Pipe[In2, Out2]): Pipe[Text, Out2]

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    Definition Classes
    Pipe

  75. def →[B](y: B): (FreeBayesParallel, B)

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

Inherited from Pipe[Text, Vcf]

Inherited from VariableResources

Inherited from ScheduleWithEmptyDefaultResources

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 FreeBayesParallel to any2stringadd[FreeBayesParallel]

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

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

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

Ungrouped