org.bdgenomics.adam.util

ReferenceContigMap

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

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

contigMap

a map containing a Seq of contig fragments per contig.

Linear Supertypes
Product, Equals, ReferenceFile, Serializable, Serializable, AnyRef, Any
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Inherited
  1. ReferenceContigMap
  2. Product
  3. Equals
  4. ReferenceFile
  5. Serializable
  6. Serializable
  7. AnyRef
  8. Any
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Instance Constructors

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

    contigMap

    a map containing a Seq of contig fragments per contig.

Value Members

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

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any
  3. final def ##(): Int

    Definition Classes
    AnyRef → Any
  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  5. final def ==(arg0: Any): Boolean

    Definition Classes
    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 contigMap: Map[String, Seq[NucleotideContigFragment]]

    a map containing a Seq of contig fragments per contig.

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

    Definition Classes
    AnyRef
  10. 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
  11. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  12. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  14. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  15. final def notify(): Unit

    Definition Classes
    AnyRef
  16. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  17. 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
  18. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  19. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  20. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  21. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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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