Class

dagr.tasks.bwa

BwaBacktrack

Related Doc: package bwa

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class BwaBacktrack extends Pipeline

Pipeline that starts with an unmapped BAM and runs through conversion to fastq, running bwa aln, bwa sampe and then MergeBamAlignment to generate a tidy mapped BAM file via bwa backtrack/bwa short alignment.

Linear Supertypes
Pipeline, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. BwaBacktrack
  2. Pipeline
  3. LazyLogging
  4. Task
  5. Dependable
  6. AnyRef
  7. 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 BwaBacktrack(unmappedBam: PathToBam, mappedBam: PathToBam, ref: PathToFasta, tmpDir: Option[DirPath] = None, maxDiffOrMissingProb: Option[Either[Int, Float]] = None, seedLength: Option[Int] = None, pairedEnd: Boolean = true)

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

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

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    Implicit information
    This member is added by an implicit conversion from BwaBacktrack to ArrowAssoc[BwaBacktrack] 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 build(): Unit

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    Strings together invocations of bwa aln and bwa sampe to generate an output SAM file.

    Strings together invocations of bwa aln and bwa sampe to generate an output SAM file.

    Definition Classes
    BwaBacktrack → Pipeline

  15. def clone(): AnyRef

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

  16. def contains(task: Task): Boolean

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    Definition Classes
    Pipeline

  17. def ensuring(cond: (BwaBacktrack) ⇒ Boolean, msg: ⇒ Any): BwaBacktrack

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

  18. def ensuring(cond: (BwaBacktrack) ⇒ Boolean): BwaBacktrack

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

  19. def ensuring(cond: Boolean, msg: ⇒ Any): BwaBacktrack

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

  20. def ensuring(cond: Boolean): BwaBacktrack

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

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

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    Definition Classes
    AnyRef

  22. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  23. def finalize(): Unit

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

  24. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  26. final def getTasks: Traversable[_ <: Task]

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    Definition Classes
    Pipeline → Task

  27. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  28. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  29. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  30. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  31. val mappedBam: PathToBam

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  32. val maxDiffOrMissingProb: Option[Either[Int, Float]]

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  33. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  35. final def notify(): Unit

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    Definition Classes
    AnyRef

  36. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  37. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  38. val outputDirectory: Option[Path]

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    Definition Classes
    Pipeline

  39. val pairedEnd: Boolean

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  40. val ref: PathToFasta

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  41. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  42. val root: Dependable

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    Definition Classes
    Pipeline

  43. val seedLength: Option[Int]

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

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    Definition Classes
    AnyRef

  45. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  46. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  47. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  48. val tmpDir: Option[DirPath]

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  49. def toString(): String

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    Definition Classes
    AnyRef → Any

  50. val unmappedBam: PathToBam

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  51. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  54. def withName(name: String): BwaBacktrack.this.type

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    Definition Classes
    Task

  55. def →[B](y: B): (BwaBacktrack, B)

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

Inherited from Pipeline

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped