Class

dagr.tasks.vc

Varscan2Somatic

Related Doc: package vc

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class Varscan2Somatic extends ProcessTask with JarTask with FixedResources with Configuration

Task for running VarScan2's somatic calling from pileup.

Linear Supertypes
Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. Varscan2Somatic
  2. Configuration
  3. ConfigurationLike
  4. FixedResources
  5. ScheduleWithEmptyDefaultResources
  6. JarTask
  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 Varscan2Somatic(tumorPileup: Path, normalPileup: Path, out: PathPrefix, minimumVariantFrequency: Double = 0.01, pValue: Double = 0.2, somaticPValue: Double = 0.05, strandFilter: Boolean = true, vcfOutput: Boolean = true)

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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 Varscan2Somatic to any2stringadd[Varscan2Somatic] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (Varscan2Somatic, B)

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to ArrowAssoc[Varscan2Somatic] 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
    Varscan2Somatic → 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. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  19. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  24. def ensuring(cond: (Varscan2Somatic) ⇒ Boolean, msg: ⇒ Any): Varscan2Somatic

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to Ensuring[Varscan2Somatic] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  25. def ensuring(cond: (Varscan2Somatic) ⇒ Boolean): Varscan2Somatic

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to Ensuring[Varscan2Somatic] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  26. def ensuring(cond: Boolean, msg: ⇒ Any): Varscan2Somatic

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to Ensuring[Varscan2Somatic] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  27. def ensuring(cond: Boolean): Varscan2Somatic

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to Ensuring[Varscan2Somatic] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  29. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  30. def finalize(): Unit

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

  31. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to StringFormat[Varscan2Somatic] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

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

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    Definition Classes
    AnyRef → Any

  33. final def getTasks: Traversable[_ <: Varscan2Somatic.this.type]

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    Definition Classes
    UnitTask → Task

  34. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  35. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  36. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  37. def jar: Path

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  38. def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

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    Attributes
    protected
    Definition Classes
    JarTask

  39. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  40. val minimumVariantFrequency: Double

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  41. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  43. val normalPileup: Path

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  44. final def notify(): Unit

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    Definition Classes
    AnyRef

  45. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  46. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

  48. val out: PathPrefix

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  49. val pValue: Double

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

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    Definition Classes
    FixedResources → Schedulable

  51. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  52. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  53. def requires(cores: Double, memory: String): Varscan2Somatic.this.type

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    Definition Classes
    FixedResources

  54. def requires(cores: Cores, memory: Memory): Varscan2Somatic.this.type

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    Definition Classes
    FixedResources

  55. def requires(resources: ResourceSet): Varscan2Somatic.this.type

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    Definition Classes
    FixedResources

  56. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

  57. val somaticPValue: Double

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  58. val strandFilter: Boolean

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

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    Definition Classes
    AnyRef

  60. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  61. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  62. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  63. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  64. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  65. val tumorPileup: Path

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  66. val vcfOutput: Boolean

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  67. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  70. def withName(name: String): Varscan2Somatic.this.type

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    Definition Classes
    Task

  71. def →[B](y: B): (Varscan2Somatic, B)

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    Implicit information
    This member is added by an implicit conversion from Varscan2Somatic to ArrowAssoc[Varscan2Somatic] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from JarTask

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 Varscan2Somatic to any2stringadd[Varscan2Somatic]

Inherited by implicit conversion StringFormat from Varscan2Somatic to StringFormat[Varscan2Somatic]

Inherited by implicit conversion Ensuring from Varscan2Somatic to Ensuring[Varscan2Somatic]

Inherited by implicit conversion ArrowAssoc from Varscan2Somatic to ArrowAssoc[Varscan2Somatic]

Ungrouped