Class

dagr.tasks.samtools

SamtoolsPileup

Related Doc: package samtools

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class SamtoolsPileup extends SamtoolsTask with FixedResources

Runs samtools pileup.

Linear Supertypes
FixedResources, ScheduleWithEmptyDefaultResources, SamtoolsTask, Configuration, ConfigurationLike, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. SamtoolsPileup
  2. FixedResources
  3. ScheduleWithEmptyDefaultResources
  4. SamtoolsTask
  5. Configuration
  6. ConfigurationLike
  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 SamtoolsPileup(ref: PathToFasta, regions: Option[PathToIntervals] = None, bam: PathToBam, out: Option[Path], maxDepth: Int = 5000, minMappingQuality: Int = 1, minBaseQuality: Int = 13)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  3. def !=>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  4. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  5. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from SamtoolsPileup to any2stringadd[SamtoolsPileup] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  6. def ->[B](y: B): (SamtoolsPileup, B)

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

  7. def ::(other: Task): MultiTask

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef → Any

  9. def ==>(other: MultiTask): other.type

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    Definition Classes
    Task → Dependable

  10. def ==>(other: Task): other.type

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    Definition Classes
    Task → Dependable

  11. def addSubcommandArgs(buffer: ListBuffer[Any]): Unit

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    Definition Classes
    SamtoolsPileup → SamtoolsTask

  12. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable

  13. def args: Seq[Any]

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    Definition Classes
    SamtoolsTask → ProcessTask

  14. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  16. def clone(): AnyRef

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

  17. val command: String

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    Definition Classes
    SamtoolsTask

  18. def commandLineName: String

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    Definition Classes
    ConfigurationLike

  19. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  23. def configureExecutableFromBinDirectory(binPath: String, executable: String): Path

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    Definition Classes
    ConfigurationLike

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

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

  25. def ensuring(cond: (SamtoolsPileup) ⇒ Boolean): SamtoolsPileup

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

  26. def ensuring(cond: Boolean, msg: ⇒ Any): SamtoolsPileup

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

  27. def ensuring(cond: Boolean): SamtoolsPileup

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

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

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    Definition Classes
    AnyRef

  29. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  30. def finalize(): Unit

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

  31. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  33. final def getTasks: Traversable[_ <: SamtoolsPileup.this.type]

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    Definition Classes
    UnitTask → Task

  34. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  35. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  36. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  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. final def notify(): Unit

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    Definition Classes
    AnyRef

  40. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  41. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    FixedResources → Schedulable

  44. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  45. def requires(cores: Double, memory: String): SamtoolsPileup.this.type

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    Definition Classes
    FixedResources

  46. def requires(cores: Cores, memory: Memory): SamtoolsPileup.this.type

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    Definition Classes
    FixedResources

  47. def requires(resources: ResourceSet): SamtoolsPileup.this.type

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    Definition Classes
    FixedResources

  48. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

  49. def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  51. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  52. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  53. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  56. def withName(name: String): SamtoolsPileup.this.type

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    Definition Classes
    Task

  57. def →[B](y: B): (SamtoolsPileup, B)

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

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from SamtoolsTask

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 SamtoolsPileup to any2stringadd[SamtoolsPileup]

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

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

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

Ungrouped