Class/Object

dagr.tasks.gatk

GenotypeGvcfs

Related Docs: object GenotypeGvcfs | package gatk

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class GenotypeGvcfs extends GatkTask

Genotypes one or more GVCFs concurrently.

Linear Supertypes
GatkTask, Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. GenotypeGvcfs
  2. GatkTask
  3. Configuration
  4. ConfigurationLike
  5. FixedResources
  6. ScheduleWithEmptyDefaultResources
  7. JarTask
  8. ProcessTask
  9. UnitTask
  10. Schedulable
  11. LazyLogging
  12. Task
  13. Dependable
  14. AnyRef
  15. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

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

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

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    Implicit information
    This member is added by an implicit conversion from GenotypeGvcfs to ArrowAssoc[GenotypeGvcfs] 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 addWalkerArgs(buffer: ListBuffer[Any]): Unit

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    Attributes
    protected
    Definition Classes
    GenotypeGvcfs → GatkTask

  13. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  14. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable

  15. def args: Seq[Any]

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    Definition Classes
    GatkTask → ProcessTask

  16. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  18. val bamCompression: Option[Int]

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    Definition Classes
    GatkTask

  19. def clone(): AnyRef

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

  20. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  21. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  26. val dbSnpVcf: Option[PathToVcf]

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

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

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

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

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

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

  30. def ensuring(cond: Boolean): GenotypeGvcfs

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

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

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    Definition Classes
    AnyRef

  32. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  33. def finalize(): Unit

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

  34. def formatted(fmtstr: String): String

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

  35. 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
    Definition Classes
    GatkTask

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

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    Definition Classes
    AnyRef → Any

  37. final def getTasks: Traversable[_ <: GenotypeGvcfs.this.type]

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    Definition Classes
    UnitTask → Task

  38. val gvcfs: Seq[PathToVcf]

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  39. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  40. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  41. val intervals: Option[PathToIntervals]

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    Definition Classes
    GatkTask

  42. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  43. 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

  44. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  45. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  47. final def notify(): Unit

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    Definition Classes
    AnyRef

  48. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  49. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    FixedResources → Schedulable

  52. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  53. val ref: PathToFasta

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    Definition Classes
    GatkTask

  54. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  55. def requires(cores: Double, memory: String): GenotypeGvcfs.this.type

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    Definition Classes
    FixedResources

  56. def requires(cores: Cores, memory: Memory): GenotypeGvcfs.this.type

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    Definition Classes
    FixedResources

  57. def requires(resources: ResourceSet): GenotypeGvcfs.this.type

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    Definition Classes
    FixedResources

  58. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

  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 vcf: PathToVcf

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  66. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  69. val walker: String

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    Definition Classes
    GatkTask

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

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    Definition Classes
    Task

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

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

Inherited from GatkTask

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 GenotypeGvcfs to any2stringadd[GenotypeGvcfs]

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

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

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

Ungrouped