Class/Object

dagr.tasks.vc

Strelka

Related Docs: object Strelka | package vc

Permalink

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
Ordering
  1. Alphabetic
  2. By Inheritance
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
  1. Hide All
  2. Show All
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)

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

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

    Permalink
    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: Option[Dependable]): Dependable

    Permalink
    Definition Classes
    Dependable

  7. def ::(other: Dependable): Dependable

    Permalink
    Definition Classes
    Dependable

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

    Permalink
    Definition Classes
    AnyRef → Any

  9. final def ==>(other: Option[Dependable]): Dependable

    Permalink
    Definition Classes
    Dependable

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

    Permalink
    Definition Classes
    Dependable

  11. def addDependent(dependent: Dependable): Unit

    Permalink
    Definition Classes
    Task → Dependable

  12. def allTasks: Traversable[Task]

    Permalink
    Definition Classes
    Task → Dependable

  13. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

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

    Permalink
    Attributes
    protected
    Definition Classes
    ConfigurationLike

  15. def build(): Unit

    Permalink
    Definition Classes
    Strelka → Pipeline

  16. def clone(): AnyRef

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

  17. def commandLineName(name: String): String

    Permalink
    Definition Classes
    ConfigurationLike

  18. def config: Config

    Permalink
    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

  19. val configFile: FilePath

    Permalink

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

  24. def contains(task: Task): Boolean

    Permalink
    Definition Classes
    Pipeline

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

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

    Permalink
    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

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

    Permalink
    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

  28. def ensuring(cond: Boolean): Strelka

    Permalink
    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

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

    Permalink
    Definition Classes
    AnyRef

  30. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  31. def finalize(): Unit

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

  32. def formatted(fmtstr: String): String

    Permalink
    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()

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

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    Pipeline → Task

  35. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  36. def headTasks: Traversable[Task]

    Permalink
    Definition Classes
    Task → Dependable

  37. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  38. lazy val logger: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    LazyLogging

  39. val maxThreads: Int

    Permalink

  40. val minThreads: Int

    Permalink

  41. var name: String

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    AnyRef

  43. val normal: PathToBam

    Permalink

  44. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  45. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  46. def onComplete(exitCode: Int): Boolean

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    ConfigurationLike

  48. val out: PathToVcf

    Permalink

  49. val outputDirectory: Option[Path]

    Permalink
    Definition Classes
    Pipeline

  50. val ref: PathToFasta

    Permalink

  51. def removeDependency(task: Task): Boolean

    Permalink
    Definition Classes
    Task

  52. val root: Dependable

    Permalink
    Definition Classes
    Pipeline

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

    Permalink
    Definition Classes
    AnyRef

  54. def systemPath: Seq[Path]

    Permalink
    Attributes
    protected
    Definition Classes
    ConfigurationLike

  55. def tailTasks: Traversable[Task]

    Permalink
    Definition Classes
    Task → Dependable

  56. def tasksDependedOn: Traversable[Task]

    Permalink
    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  57. def tasksDependingOnThisTask: Traversable[Task]

    Permalink
    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  58. val tmp: Option[DirPath]

    Permalink

  59. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  60. val tumor: PathToBam

    Permalink

  61. final def wait(): Unit

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

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

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

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

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

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

    Permalink
    Definition Classes
    Task

  65. def →[B](y: B): (Strelka, B)

    Permalink
    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