Class

dagr.tasks.vc

FreeBayesGermline

Related Doc: package vc

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class FreeBayesGermline extends FreeBayes

Performs Germline variant calling using FreeBayes according the the BCBIO best Practices

Linear Supertypes
FreeBayes, VariableResources, ScheduleWithEmptyDefaultResources, Schedulable, Configuration, ConfigurationLike, LazyLogging, Task, Dependable, AnyRef, Any
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  2. By inheritance
Inherited
  1. FreeBayesGermline
  2. FreeBayes
  3. VariableResources
  4. ScheduleWithEmptyDefaultResources
  5. Schedulable
  6. Configuration
  7. ConfigurationLike
  8. LazyLogging
  9. Task
  10. Dependable
  11. AnyRef
  12. 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 FreeBayesGermline(ref: PathToFasta, targetIntervals: Option[PathToIntervals], bam: List[PathToBam], vcf: PathToVcf, compress: Boolean = true, memory: Memory = DefaultMemory, minThreads: Int = DefaultMinThreads, maxThreads: Int = DefaultMaxThreads, regionSize: Long = DefaultRegionSize, useBestNAlleles: Option[Int] = DefaultUseBestNAlleles, maxCoverage: Option[Int] = DefaultMaxCoverage, minRepeatEntropy: Option[Int] = DefaultMinRepeatEntropy)

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

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

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    Implicit information
    This member is added by an implicit conversion from FreeBayesGermline to ArrowAssoc[FreeBayesGermline] 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 applyResources(resources: ResourceSet): Unit

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    Definition Classes
    VariableResources → Schedulable

  12. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  14. val bam: List[PathToBam]

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    Definition Classes
    FreeBayes

  15. def clone(): AnyRef

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

  16. def commandLineName: String

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    Definition Classes
    ConfigurationLike

  17. val compress: Boolean

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    Definition Classes
    FreeBayes

  18. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  23. def ensuring(cond: (FreeBayesGermline) ⇒ Boolean, msg: ⇒ Any): FreeBayesGermline

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

  24. def ensuring(cond: (FreeBayesGermline) ⇒ Boolean): FreeBayesGermline

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

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

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

  26. def ensuring(cond: Boolean): FreeBayesGermline

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

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

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    Definition Classes
    AnyRef

  28. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  29. def finalize(): Unit

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

  30. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  32. def getTasks: Traversable[_ <: Task]

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    Sets the arguments for FreeBayes.

    Sets the arguments for FreeBayes. For somatic calling, there should be two bams, a tumor bam then normal bam.

    Definition Classes
    FreeBayes → Task

  33. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  34. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  35. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  36. val maxCoverage: Option[Int]

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    Definition Classes
    FreeBayes

  37. val maxThreads: Int

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    Definition Classes
    FreeBayes

  38. val memory: Memory

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    Definition Classes
    FreeBayes

  39. val minRepeatEntropy: Option[Int]

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    Definition Classes
    FreeBayes

  40. val minThreads: Int

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    Definition Classes
    FreeBayes

  41. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  43. final def notify(): Unit

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    Definition Classes
    AnyRef

  44. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  45. def numThreads: Int

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    Attributes
    protected
    Definition Classes
    FreeBayes

  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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    Attempts to pick the resources required to run.

    Attempts to pick the resources required to run. The required resources are: 1) Cores = the cores for freebayes plus one additional core to account for the other scripts 2) Memory = a fixed amount.

    Definition Classes
    FreeBayes → Schedulable

  49. val ref: PathToFasta

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    Definition Classes
    FreeBayes

  50. val regionSize: Long

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    Definition Classes
    FreeBayes

  51. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  52. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    Task

  54. val somatic: Boolean

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    Definition Classes
    FreeBayes

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

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    Definition Classes
    AnyRef

  56. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  57. val targetIntervals: Option[PathToIntervals]

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    Definition Classes
    FreeBayes

  58. def toString(): String

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    Definition Classes
    AnyRef → Any

  59. val useBestNAlleles: Option[Int]

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    Definition Classes
    FreeBayes

  60. val vcf: PathToVcf

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    Definition Classes
    FreeBayes

  61. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    Task

  65. def →[B](y: B): (FreeBayesGermline, B)

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

Inherited from FreeBayes

Inherited from VariableResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from Schedulable

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from FreeBayesGermline to any2stringadd[FreeBayesGermline]

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

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

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

Ungrouped