Class/Object

org.bdgenomics.adam.util

ReferenceContigMap

Related Docs: object ReferenceContigMap | package util

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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
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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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Visibility
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Instance Constructors

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

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    contigMap

    a map containing a Seq of slices per contig.

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

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def clone(): AnyRef

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

  6. val contigMap: Map[String, Seq[Slice]]

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    a map containing a Seq of slices per contig.

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

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    Definition Classes
    AnyRef

  8. def extract(region: ReferenceRegion): String

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    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
    ReferenceContigMap → ReferenceFile

  9. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  11. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  13. final def notify(): Unit

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    Definition Classes
    AnyRef

  14. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  15. val sequences: SequenceDictionary

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    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
    ReferenceContigMap → ReferenceFile

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

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    Definition Classes
    AnyRef

  17. def toString(): String

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    Definition Classes
    ReferenceContigMap → AnyRef → Any

  18. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    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

Ungrouped