Class/Object

dagr.tasks.vc

Strelka

Related Docs: object Strelka | package vc

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class Strelka extends Pipeline with Configuration with LazyLogging

Runs the Strelka somatic variant caller from Illumina, cleans up after it and merges the results into a single VCF for downstream analysis.

Linear Supertypes
Configuration, ConfigurationLike, Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. Strelka
  2. Configuration
  3. ConfigurationLike
  4. Pipeline
  5. LazyLogging
  6. Task
  7. Dependable
  8. AnyRef
  9. 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 Strelka(tumor: PathToBam, normal: PathToBam, configFile: FilePath, ref: PathToFasta, out: PathToVcf, tmp: Option[DirPath], minThreads: Int = 1, maxThreads: Int = 8)

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

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

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    Implicit information
    This member is added by an implicit conversion from Strelka to ArrowAssoc[Strelka] 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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  12. def build(): Unit

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    Definition Classes
    Strelka → Pipeline

  13. def clone(): AnyRef

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

  14. def commandLineName: String

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    Definition Classes
    ConfigurationLike

  15. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

  16. val configFile: FilePath

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  21. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  22. def ensuring(cond: (Strelka) ⇒ Boolean, msg: ⇒ Any): Strelka

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

  23. def ensuring(cond: (Strelka) ⇒ Boolean): Strelka

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

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

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

  25. def ensuring(cond: Boolean): Strelka

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

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

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    Definition Classes
    AnyRef

  27. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  28. def finalize(): Unit

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

  29. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  31. final def getTasks: Traversable[_ <: Task]

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    Definition Classes
    Pipeline → Task

  32. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  33. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  34. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  35. val maxThreads: Int

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  36. val minThreads: Int

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  37. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  39. val normal: PathToBam

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  40. final def notify(): Unit

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    Definition Classes
    AnyRef

  41. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  42. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

  44. val out: PathToVcf

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  45. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  46. val ref: PathToFasta

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  47. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  48. val root: Dependable

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    Definition Classes
    Pipeline

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

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    Definition Classes
    AnyRef

  50. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  51. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  52. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  53. val tmp: Option[DirPath]

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  54. def toString(): String

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    Definition Classes
    AnyRef → Any

  55. val tumor: PathToBam

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  56. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  59. def withName(name: String): Strelka.this.type

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    Definition Classes
    Task

  60. def →[B](y: B): (Strelka, B)

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

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from Pipeline

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from Strelka to any2stringadd[Strelka]

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

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

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

Ungrouped