Class

dagr.tasks.vc

FreeBayesSomatic

Related Doc: package vc

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class FreeBayesSomatic extends FreeBayes

Performs Somatic (Tumor/Normal) 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. FreeBayesSomatic
  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 FreeBayesSomatic(ref: PathToFasta, targetIntervals: Option[PathToIntervals], tumorBam: PathToBam, normalBam: 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, minAlternateAlleleFraction: Option[Float] = DefaultMinAlternateAlleleFraction)

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

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

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

  6. def ::(other: Dependable): Dependable

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    Definition Classes
    Dependable

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

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    Definition Classes
    AnyRef → Any

  8. final def ==>(other: Dependable): Dependable

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    Definition Classes
    Dependable

  9. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable

  10. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  12. val bam: List[PathToBam]

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    Definition Classes
    FreeBayes

  13. def clone(): AnyRef

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

  14. def commandLineName: String

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    Definition Classes
    ConfigurationLike

  15. val compress: Boolean

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    Definition Classes
    FreeBayes

  16. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  21. def ensuring(cond: (FreeBayesSomatic) ⇒ Boolean, msg: ⇒ Any): FreeBayesSomatic

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

  22. def ensuring(cond: (FreeBayesSomatic) ⇒ Boolean): FreeBayesSomatic

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

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

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

  24. def ensuring(cond: Boolean): FreeBayesSomatic

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

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

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    Definition Classes
    AnyRef

  26. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  27. def finalize(): Unit

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

  28. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  30. 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

  31. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  32. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  33. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  34. val maxCoverage: Option[Int]

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    Definition Classes
    FreeBayes

  35. val maxThreads: Int

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    Definition Classes
    FreeBayes

  36. val memory: Memory

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    Definition Classes
    FreeBayes

  37. val minAlternateAlleleFraction: Option[Float]

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  38. val minRepeatEntropy: Option[Int]

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    Definition Classes
    FreeBayes

  39. val minThreads: Int

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    Definition Classes
    FreeBayes

  40. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  42. final def notify(): Unit

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    Definition Classes
    AnyRef

  43. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  44. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

  46. val ref: PathToFasta

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    Definition Classes
    FreeBayes

  47. val regionSize: Long

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    Definition Classes
    FreeBayes

  48. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  49. val somatic: Boolean

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    Definition Classes
    FreeBayes

  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. val targetIntervals: Option[PathToIntervals]

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    Definition Classes
    FreeBayes

  53. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  54. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  55. def toString(): String

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    Definition Classes
    AnyRef → Any

  56. val useBestNAlleles: Option[Int]

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    Definition Classes
    FreeBayes

  57. val vcf: PathToVcf

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    Definition Classes
    FreeBayes

  58. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  61. def withName(name: String): FreeBayesSomatic.this.type

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    Definition Classes
    Task

  62. def →[B](y: B): (FreeBayesSomatic, B)

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    Implicit information
    This member is added by an implicit conversion from FreeBayesSomatic to ArrowAssoc[FreeBayesSomatic] 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 FreeBayesSomatic to any2stringadd[FreeBayesSomatic]

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

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

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

Ungrouped