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, Configuration, ConfigurationLike, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. FreeBayesGermline
  2. FreeBayes
  3. Configuration
  4. ConfigurationLike
  5. LazyLogging
  6. Task
  7. Dependable
  8. AnyRef
  9. 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: 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 FreeBayesGermline to any2stringadd[FreeBayesGermline] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. 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()

  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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  15. val bam: List[PathToBam]

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    Definition Classes
    FreeBayes

  16. def clone(): AnyRef

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

  17. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  18. val compress: Boolean

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    Definition Classes
    FreeBayes

  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, subDir: Option[Path]): Path

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    Definition Classes
    ConfigurationLike

  24. 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

  25. 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

  26. 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

  27. 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

  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 FreeBayesGermline to StringFormat[FreeBayesGermline] 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. 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

  34. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  35. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  36. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  37. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  38. val maxCoverage: Option[Int]

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    Definition Classes
    FreeBayes

  39. val maxThreads: Int

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    Definition Classes
    FreeBayes

  40. val memory: Memory

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    Definition Classes
    FreeBayes

  41. val minRepeatEntropy: Option[Int]

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    Definition Classes
    FreeBayes

  42. val minThreads: Int

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    Definition Classes
    FreeBayes

  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 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. val somatic: Boolean

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    Definition Classes
    FreeBayes

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

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    Definition Classes
    AnyRef

  54. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  55. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  56. val targetIntervals: Option[PathToIntervals]

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    Definition Classes
    FreeBayes

  57. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  58. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  59. def toString(): String

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    Definition Classes
    AnyRef → Any

  60. val useBestNAlleles: Option[Int]

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    Definition Classes
    FreeBayes

  61. val vcf: PathToVcf

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    Definition Classes
    FreeBayes

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

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    Definition Classes
    Task

  66. 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 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