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

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

contigMap

a map containing a Seq of slices per contig.

Linear Supertypes
Product, Equals, ReferenceFile, Serializable, Serializable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. ReferenceContigMap
  2. Product
  3. Equals
  4. ReferenceFile
  5. Serializable
  6. Serializable
  7. AnyRef
  8. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new ReferenceContigMap(contigMap: Map[String, Seq[Slice]])

    contigMap

    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[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  6. val contigMap: Map[String, Seq[Slice]]
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. 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
    ReferenceContigMapReferenceFile
  9. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  12. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  14. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  15. val sequences: SequenceDictionary

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

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

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

Inherited from Product

Inherited from Equals

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped