Class

dagr.tasks.misc

VerifyBamId

Related Doc: package misc

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class VerifyBamId extends ProcessTask with Configuration with FixedResources

Class for running verifyBamID on sequence data in genotype-free mode.

Linear Supertypes
FixedResources, ScheduleWithEmptyDefaultResources, Configuration, ConfigurationLike, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. VerifyBamId
  2. FixedResources
  3. ScheduleWithEmptyDefaultResources
  4. Configuration
  5. ConfigurationLike
  6. ProcessTask
  7. UnitTask
  8. Schedulable
  9. LazyLogging
  10. Task
  11. Dependable
  12. AnyRef
  13. 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 VerifyBamId(vcf: PathToVcf, bam: PathToBam, out: Path, maxDepth: Int = 50, minMapq: Int = 20, minQ: Int = 20, grid: Double = 0.01, precise: 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 VerifyBamId to any2stringadd[VerifyBamId] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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    Implicit information
    This member is added by an implicit conversion from VerifyBamId to ArrowAssoc[VerifyBamId] 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
    VerifyBamId → 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 bam: PathToBam

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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: (VerifyBamId) ⇒ Boolean, msg: ⇒ Any): VerifyBamId

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

  26. def ensuring(cond: (VerifyBamId) ⇒ Boolean): VerifyBamId

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

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

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

  28. def ensuring(cond: Boolean): VerifyBamId

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

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

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    Definition Classes
    AnyRef → Any

  34. final def getTasks: Traversable[_ <: VerifyBamId.this.type]

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    Definition Classes
    UnitTask → Task

  35. val grid: Double

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  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. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  39. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  40. val maxDepth: Int

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  41. val minMapq: Int

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  42. val minQ: Int

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  43. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  45. final def notify(): Unit

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    Definition Classes
    AnyRef

  46. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  47. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

  49. val out: Path

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

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    Definition Classes
    FixedResources → Schedulable

  51. val precise: Boolean

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  52. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  53. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  54. def requires(cores: Double, memory: String): VerifyBamId.this.type

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    Definition Classes
    FixedResources

  55. def requires(cores: Cores, memory: Memory): VerifyBamId.this.type

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    Definition Classes
    FixedResources

  56. def requires(resources: ResourceSet): VerifyBamId.this.type

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    Definition Classes
    FixedResources

  57. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  59. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  60. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  61. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  62. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  63. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  64. val vcf: PathToVcf

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  65. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  68. def withName(name: String): VerifyBamId.this.type

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    Definition Classes
    Task

  69. def →[B](y: B): (VerifyBamId, B)

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

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from Configuration

Inherited from ConfigurationLike

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 VerifyBamId to any2stringadd[VerifyBamId]

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

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

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

Ungrouped