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: PathToBam, ref: PathToFasta, intervals: PathToIntervals, dbsnpVcf: Option[PathToVcf] = None, vcfOutput: PathToVcf, callStatsOutput: Path, tumorSampleName: String = "tumor", normalSampleName: String = "normal", fractionContamination: Double = 0, maxAltAlleleInNormalFraction: Double = 0.03, maxAltAlleleInNormalCount: Int = 5, maxAltAlleleInNormalBqSum: Int = 40)

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

  6. 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()

  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 addWalkerArgs(buffer: ListBuffer[Any]): Unit

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    Attributes
    protected
    Definition Classes
    Mutect1 → GatkTask

  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
    GatkTask → 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. val callStatsOutput: Path

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  17. def clone(): AnyRef

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

  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. val dbsnpVcf: Option[PathToVcf]

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  25. 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

  26. 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

  27. 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

  28. 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

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

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    Definition Classes
    AnyRef

  30. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  31. def finalize(): Unit

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

  32. 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()

  33. val fractionContamination: Double

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  34. 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

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

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    UnitTask → Task

  37. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  38. val intervals: Option[PathToIntervals]

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    Definition Classes
    GatkTask

  39. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  40. 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

  41. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  42. val maxAltAlleleInNormalBqSum: Int

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  43. val maxAltAlleleInNormalCount: Int

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  44. val maxAltAlleleInNormalFraction: Double

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  45. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  47. val normalBam: PathToBam

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  48. val normalSampleName: String

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  49. final def notify(): Unit

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    Definition Classes
    AnyRef

  50. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  51. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    FixedResources → Schedulable

  54. val ref: PathToFasta

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    Definition Classes
    GatkTask

  55. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    FixedResources

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

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    Definition Classes
    FixedResources

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

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    Definition Classes
    FixedResources

  59. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  62. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  63. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  64. val tumorBam: PathToBam

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  65. val tumorSampleName: String

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  66. val vcfOutput: PathToVcf

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  67. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  70. val walker: String

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    Definition Classes
    GatkTask

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

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    Definition Classes
    Task

  72. 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