Class

dagr.tasks.gatk

Mutect1

Related Doc: package gatk

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class Mutect1 extends GatkTask

Runs Mutect 1 from the separate Mutect/CGA tools distribution

Linear Supertypes
GatkTask, Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. Mutect1
  2. GatkTask
  3. Configuration
  4. ConfigurationLike
  5. FixedResources
  6. ScheduleWithEmptyDefaultResources
  7. JarTask
  8. ProcessTask
  9. UnitTask
  10. Schedulable
  11. LazyLogging
  12. Task
  13. Dependable
  14. AnyRef
  15. 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 Mutect1(tumorBam: PathToBam, normalBam: Option[PathToBam] = None, ref: PathToFasta, intervals: PathToIntervals, dbsnpVcf: Option[PathToVcf] = None, vcfOutput: PathToVcf, callStatsOutput: Path, tumorSampleName: String = "tumor", normalSampleName: String = "normal", minimumAf: Option[Double] = None, fractionContamination: Double = 0, maxAltAlleleInNormalFraction: Double = 0.03, maxAltAlleleInNormalCount: Int = 5, maxAltAlleleInNormalBqSum: Int = 40, minBaseQuality: Int = 5)

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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 Mutect1 to any2stringadd[Mutect1] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (Mutect1, B)

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to ArrowAssoc[Mutect1] 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 addWalkerArgs(buffer: ListBuffer[Any]): Unit

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    Attributes
    protected
    Definition Classes
    Mutect1 → GatkTask

  13. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  14. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable

  15. def args: Seq[Any]

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    Definition Classes
    GatkTask → ProcessTask

  16. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  18. val bamCompression: Option[Int]

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    Definition Classes
    GatkTask

  19. val callStatsOutput: Path

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  20. def clone(): AnyRef

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

  21. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  22. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  27. val dbsnpVcf: Option[PathToVcf]

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  28. def ensuring(cond: (Mutect1) ⇒ Boolean, msg: ⇒ Any): Mutect1

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to Ensuring[Mutect1] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  29. def ensuring(cond: (Mutect1) ⇒ Boolean): Mutect1

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to Ensuring[Mutect1] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  30. def ensuring(cond: Boolean, msg: ⇒ Any): Mutect1

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to Ensuring[Mutect1] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  31. def ensuring(cond: Boolean): Mutect1

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to Ensuring[Mutect1] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  33. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  34. def finalize(): Unit

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

  35. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to StringFormat[Mutect1] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

  36. val fractionContamination: Double

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  37. def gatkJar: Path

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    Use a custom JAR for running Mutect1.

    Use a custom JAR for running Mutect1.

    Attributes
    protected
    Definition Classes
    Mutect1 → GatkTask

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

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    Definition Classes
    AnyRef → Any

  39. final def getTasks: Traversable[_ <: Mutect1.this.type]

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    Definition Classes
    UnitTask → Task

  40. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  41. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  42. val intervals: Option[PathToIntervals]

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    Definition Classes
    GatkTask

  43. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  44. def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

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    Attributes
    protected
    Definition Classes
    JarTask

  45. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  46. val maxAltAlleleInNormalBqSum: Int

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  47. val maxAltAlleleInNormalCount: Int

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  48. val maxAltAlleleInNormalFraction: Double

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  49. val minBaseQuality: Int

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  50. val minimumAf: Option[Double]

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  51. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  53. val normalBam: Option[PathToBam]

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  54. val normalSampleName: String

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  55. final def notify(): Unit

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    Definition Classes
    AnyRef

  56. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  57. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    FixedResources → Schedulable

  60. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  61. val ref: PathToFasta

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    Definition Classes
    GatkTask

  62. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  63. def requires(cores: Double, memory: String): Mutect1.this.type

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    Definition Classes
    FixedResources

  64. def requires(cores: Cores, memory: Memory): Mutect1.this.type

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    Definition Classes
    FixedResources

  65. def requires(resources: ResourceSet): Mutect1.this.type

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    Definition Classes
    FixedResources

  66. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  68. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  69. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  70. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  71. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  72. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  73. val tumorBam: PathToBam

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  74. val tumorSampleName: String

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  75. val vcfOutput: PathToVcf

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  76. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  79. val walker: String

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    Definition Classes
    GatkTask

  80. def withName(name: String): Mutect1.this.type

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    Definition Classes
    Task

  81. def →[B](y: B): (Mutect1, B)

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    Implicit information
    This member is added by an implicit conversion from Mutect1 to ArrowAssoc[Mutect1] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from GatkTask

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from JarTask

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 Mutect1 to any2stringadd[Mutect1]

Inherited by implicit conversion StringFormat from Mutect1 to StringFormat[Mutect1]

Inherited by implicit conversion Ensuring from Mutect1 to Ensuring[Mutect1]

Inherited by implicit conversion ArrowAssoc from Mutect1 to ArrowAssoc[Mutect1]

Ungrouped