case class ReferenceMap(referenceMap: Map[String, Seq[Slice]]) extends ReferenceFile with Product with Serializable

A broadcastable ReferenceFile backed by a map containing reference name -> Seq[Slice] pairs.

referenceMap

a map containing a Seq of slices per contig.

Linear Supertypes
Product, Equals, ReferenceFile, Serializable, Serializable, AnyRef, Any
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Inherited
  1. ReferenceMap
  2. Product
  3. Equals
  4. ReferenceFile
  5. Serializable
  6. Serializable
  7. AnyRef
  8. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new ReferenceMap(referenceMap: Map[String, Seq[Slice]])

    referenceMap

    a map containing a Seq of slices per contig.

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def extract(region: ReferenceRegion): String

    Extract reference sequence from the file.

    Extract reference sequence from the file.

    region

    The desired ReferenceRegion to extract.

    returns

    The reference sequence at the desired locus.

    Definition Classes
    ReferenceMapReferenceFile
  8. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  9. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  10. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  11. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  12. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  13. val referenceMap: Map[String, Seq[Slice]]
  14. val references: SequenceDictionary

    The reference sequence dictionary corresponding to the contigs in this collection of fragments.

    The reference sequence dictionary corresponding to the contigs in this collection of fragments.

    Definition Classes
    ReferenceMapReferenceFile
  15. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  16. def toString(): String
    Definition Classes
    ReferenceMap → AnyRef → Any
  17. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  18. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  19. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from Product

Inherited from Equals

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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