Class

dagr.tasks.vc

FreeBayesParallel

Related Doc: package vc

Permalink

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
Ordering
  1. Alphabetic
  2. By inheritance
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
  1. Hide All
  2. Show all
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)

    Permalink

Value Members

  1. final def !=(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  2. def !=>(other: Dependable): Unit

    Permalink
    Definition Classes
    Task → Dependable

  3. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  4. def +(other: String): String

    Permalink
    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)

    Permalink
    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: Dependable): Dependable

    Permalink
    Definition Classes
    Dependable

  7. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  8. final def ==>(other: Dependable): Dependable

    Permalink
    Definition Classes
    Dependable

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

    Permalink
    Definition Classes
    Pipe

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

    Permalink
    Definition Classes
    Pipe

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

    Permalink
    Definition Classes
    Pipe

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

    Permalink
    Definition Classes
    Pipe

  13. def addDependent(dependent: Dependable): Unit

    Permalink
    Definition Classes
    Task → Dependable

  14. def applyResources(resources: ResourceSet): Unit

    Permalink
    Definition Classes
    VariableResources → Schedulable

  15. def args: Seq[Any]

    Permalink
    Definition Classes
    FreeBayesParallel → ProcessTask

  16. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

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

    Permalink
    Attributes
    protected
    Definition Classes
    ConfigurationLike

  18. val bam: List[PathToBam]

    Permalink

  19. def clone(): AnyRef

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

  20. def commandLineName: String

    Permalink
    Definition Classes
    ConfigurationLike

  21. def config: Config

    Permalink
    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    Pipe

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

    Permalink
    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

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

    Permalink
    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

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

    Permalink
    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

  30. def ensuring(cond: Boolean): FreeBayesParallel

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

    Permalink
    Definition Classes
    AnyRef

  32. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  33. def finalize(): Unit

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

  34. def formatted(fmtstr: String): String

    Permalink
    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()

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

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    UnitTask → Task

  37. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  38. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  39. lazy val logger: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    LazyLogging

  40. val maxCoverage: Option[Int]

    Permalink

  41. val maxThreads: Int

    Permalink

  42. val memory: Memory

    Permalink

  43. val minAlternateAlleleFraction: Option[Float]

    Permalink

  44. val minRepeatEntropy: Option[Int]

    Permalink

  45. val minThreads: Int

    Permalink

  46. var name: String

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    AnyRef

  48. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  49. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  50. def numThreads: Int

    Permalink
    Attributes
    protected

  51. def onComplete(exitCode: Int): Boolean

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink

    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

  54. var quoteIfNecessary: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    ProcessTask

  55. val ref: PathToFasta

    Permalink

  56. def removeDependency(task: Task): Boolean

    Permalink
    Definition Classes
    Task

  57. def resources: ResourceSet

    Permalink
    Definition Classes
    ScheduleWithEmptyDefaultResources

  58. val somatic: Boolean

    Permalink

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

    Permalink
    Definition Classes
    AnyRef

  60. def systemPath: Seq[Path]

    Permalink
    Attributes
    protected
    Definition Classes
    ConfigurationLike

  61. def tasksDependedOn: Traversable[Task]

    Permalink
    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  62. def tasksDependingOnThisTask: Traversable[Task]

    Permalink
    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  63. def toString(): String

    Permalink
    Definition Classes
    ProcessTask → AnyRef → Any

  64. val useBestNAlleles: Option[Int]

    Permalink

  65. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    Pipe

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

    Permalink
    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