class VariantMask extends AnyRef

Simple mask that loads variants one reference sequence at a time and creates a compact representation allowing for rapid querying of whether or not positions are overlapped by one or more variants.

Linear Supertypes
AnyRef, Any
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Inherited
  1. VariantMask
  2. AnyRef
  3. 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 VariantMask(variants: Iterator[VariantContext], dict: SAMSequenceDictionary)

    variants

    a coordinate sorted iterator of variants

    dict

    the sequence dictionary for the reference

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from VariantMask to any2stringadd[VariantMask] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (VariantMask, B)
    Implicit
    This member is added by an implicit conversion from VariantMask to ArrowAssoc[VariantMask] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. val dict: SAMSequenceDictionary
  9. def ensuring(cond: (VariantMask) ⇒ Boolean, msg: ⇒ Any): VariantMask
    Implicit
    This member is added by an implicit conversion from VariantMask to Ensuring[VariantMask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (VariantMask) ⇒ Boolean): VariantMask
    Implicit
    This member is added by an implicit conversion from VariantMask to Ensuring[VariantMask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): VariantMask
    Implicit
    This member is added by an implicit conversion from VariantMask to Ensuring[VariantMask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): VariantMask
    Implicit
    This member is added by an implicit conversion from VariantMask to Ensuring[VariantMask] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  15. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from VariantMask to StringFormat[VariantMask] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  18. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  19. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  20. def isVariant(refName: String, position: Int): Boolean

    Returns true if the position is overlapped by one or more variants, false otherwise.

  21. def isVariant(refIndex: Int, position: Int): Boolean

    Returns true if the position is overlapped by one or more variants, false otherwise.

  22. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  23. final def notify(): Unit
    Definition Classes
    AnyRef
  24. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toString(): String
    Definition Classes
    AnyRef → Any
  27. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. def →[B](y: B): (VariantMask, B)
    Implicit
    This member is added by an implicit conversion from VariantMask to ArrowAssoc[VariantMask] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped