ADAM_2.12: Core 1.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package util
  Definition Classes
    adam
- ADAMShell
- AttributeUtils
- FileExtensions
- GenomeFileReader
- IndexedFastaFile
- ParquetFileTraversable
- ParquetLogger
- PhredUtils
- ReferenceFile
- ReferenceMap
- ReferenceMapSerializer
- SequenceDictionaryReader
- TextRddWriter
- TwoBitFile
- TwoBitFileSerializer

c

org.bdgenomics.adam.util

# ReferenceMap 

###
Companion object ReferenceMap

#### 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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Ordering

1. Alphabetic
2. By Inheritance

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()
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
     ReferenceMap → ReferenceFile
8.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )
9.  final def getClass(): Class[_]
   Definition Classes
     AnyRef → Any
   Annotations
     @native()
10.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
11.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
12.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
13.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
14.  val referenceMap: Map[String, Seq[Slice]]
15.  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
      ReferenceMap → ReferenceFile
16.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
17.  def toString(): String
    Definition Classes
      ReferenceMap → 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
      @throws( ... ) @native()

### Inherited from Product

### Inherited from Equals

### Inherited from ReferenceFile

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped