org.bdgenomics.adam.util

# ReferenceContigMap

###
Related Docs: object ReferenceContigMap | package util

#### 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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Visibility

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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: 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
     @throws( ... )

6. #### val contigMap: Map[String, Seq[NucleotideContigFragment]]

   a map containing a Seq of contig fragments per contig.

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
     ReferenceContigMap → ReferenceFile

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

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

14. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

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
      ReferenceContigMap → ReferenceFile

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

    Definition Classes
      AnyRef

17. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

19. #### 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 AnyRef

### Inherited from Any

### Ungrouped