Class

com.fulcrumgenomics.bam.FindSwitchbackReads

TandemBasedHit

Related Doc: package FindSwitchbackReads

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case class TandemBasedHit(gap: Int) extends SwitchHit with Product with Serializable

Information about a switchback found by examining a template with a tandem (i.e. FF or RR) pair orientation. The offset in this case is the distance between the end of one read and the beginning of the next. E.g.

01234567890123456789 -----> -----> gap = 2 <----- <----- gap = 1 -----> ------> gap = -2

gap

the unsequenced gap between the the 3' end of the "earlier" read and the 5' end of the "later" read.

Linear Supertypes
Serializable, Serializable, Product, Equals, SwitchHit, AnyRef, Any
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Inherited
  1. TandemBasedHit
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. SwitchHit
  7. AnyRef
  8. 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 TandemBasedHit(gap: Int)

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    gap

    the unsequenced gap between the the 3' end of the "earlier" read and the 5' end of the "later" read.

Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from TandemBasedHit to any2stringadd[TandemBasedHit] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  4. def ->[B](y: B): (TandemBasedHit, B)

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

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

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    Definition Classes
    AnyRef → Any

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. val code: Char

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    Definition Classes
    TandemBasedHit → SwitchHit

  9. def ensuring(cond: (TandemBasedHit) ⇒ Boolean, msg: ⇒ Any): TandemBasedHit

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

  10. def ensuring(cond: (TandemBasedHit) ⇒ Boolean): TandemBasedHit

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

  11. def ensuring(cond: Boolean, msg: ⇒ Any): TandemBasedHit

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

  12. def ensuring(cond: Boolean): TandemBasedHit

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

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

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    Definition Classes
    AnyRef

  14. def finalize(): Unit

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

  15. def formatted(fmtstr: String): String

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

  16. val gap: Int

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    the unsequenced gap between the the 3' end of the "earlier" read and the 5' end of the "later" read.

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

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    Definition Classes
    AnyRef → Any

  18. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  20. final def notify(): Unit

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    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    AnyRef

  23. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  26. def →[B](y: B): (TandemBasedHit, B)

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

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from SwitchHit

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped