Class/Object

dagr.tasks.gatk

GatkTask

Related Docs: object GatkTask | package gatk

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abstract class GatkTask extends ProcessTask with JarTask with FixedResources with Configuration

Abstract base class for tasks that involve running the GATK.

Linear Supertypes
Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
Known Subclasses
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. GatkTask
  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 GatkTask(walker: String, ref: PathToFasta, intervals: Option[PathToIntervals] = None, bamCompression: Option[Int] = None)

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Abstract Value Members

  1. abstract def addWalkerArgs(buffer: ListBuffer[Any]): Unit

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    Attributes
    protected

Concrete 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 GatkTask to any2stringadd[GatkTask] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  5. def ->[B](y: B): (GatkTask, B)

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    Implicit information
    This member is added by an implicit conversion from GatkTask to ArrowAssoc[GatkTask] 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
    GatkTask → 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. val bamCompression: Option[Int]

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  18. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  19. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike
  20. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike
  21. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  22. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  23. def configureExecutable(path: String, executable: String): Path

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    Definition Classes
    ConfigurationLike
  24. def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

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    Definition Classes
    ConfigurationLike
  25. def ensuring(cond: (GatkTask) ⇒ Boolean, msg: ⇒ Any): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  26. def ensuring(cond: (GatkTask) ⇒ Boolean): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  27. def ensuring(cond: Boolean, msg: ⇒ Any): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  28. def ensuring(cond: Boolean): GatkTask

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    Implicit information
    This member is added by an implicit conversion from GatkTask to Ensuring[GatkTask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  29. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  30. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  31. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  32. def formatted(fmtstr: String): String

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

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    Can be overridden to use a specific GATK jar.

    Can be overridden to use a specific GATK jar.

    Attributes
    protected
  34. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  35. final def getTasks: Traversable[_ <: GatkTask.this.type]

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    Definition Classes
    UnitTask → Task
  36. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  37. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable
  38. val intervals: Option[PathToIntervals]

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  39. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  40. 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
  41. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging
  42. var name: String

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    Definition Classes
    Task
  43. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  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. def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    FixedResources → Schedulable
  49. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask
  50. val ref: PathToFasta

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  51. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task
  52. def requires(cores: Double, memory: String): GatkTask.this.type

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    Definition Classes
    FixedResources
  53. def requires(cores: Cores, memory: Memory): GatkTask.this.type

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    Definition Classes
    FixedResources
  54. def requires(resources: ResourceSet): GatkTask.this.type

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    Definition Classes
    FixedResources
  55. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources
  56. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  57. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  58. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable
  59. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task
  60. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task
  61. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any
  62. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  63. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  64. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  65. val walker: String

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  66. def withName(name: String): GatkTask.this.type

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    Definition Classes
    Task
  67. def [B](y: B): (GatkTask, B)

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    Implicit information
    This member is added by an implicit conversion from GatkTask to ArrowAssoc[GatkTask] 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 GatkTask to any2stringadd[GatkTask]

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

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

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

Ungrouped