ADAM_2.12: Core 0.32.0 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
- ReferenceContigMap
- ReferenceContigMapSerializer
- ReferenceFile
- SequenceDictionaryReader
- TextRddWriter
- TwoBitFile
- TwoBitFileSerializer

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org.bdgenomics.adam.util

# ReferenceFile 

###

#### trait ReferenceFile extends Serializable

File that contains a reference assembly that can be broadcasted

Linear Supertypes
Serializable, Serializable, AnyRef, Any
Known Subclasses
IndexedFastaFile, ReferenceContigMap, TwoBitFile
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### Abstract Value Members

1.  abstract 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.

2.  abstract def sequences: SequenceDictionary

### Concrete 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
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     AnyRef → Any
4.  final def asInstanceOf[T0]: T0
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     Any
5.  def clone(): AnyRef
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     protected[java.lang]
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     @native() @throws( ... )
6.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
7.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
8.  def finalize(): Unit
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     protected[java.lang]
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   Annotations
     @throws( classOf[java.lang.Throwable] )
9.  final def getClass(): Class[_]
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   Annotations
     @native()
10.  def hashCode(): Int
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    Annotations
      @native()
11.  final def isInstanceOf[T0]: Boolean
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      Any
12.  final def ne(arg0: AnyRef): Boolean
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13.  final def notify(): Unit
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      @native()
14.  final def notifyAll(): Unit
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      @native()
15.  final def synchronized[T0](arg0: ⇒ T0): T0
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16.  def toString(): String
    Definition Classes
      AnyRef → Any
17.  final def wait(): Unit
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      AnyRef
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      @throws( ... )
18.  final def wait(arg0: Long, arg1: Int): Unit
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    Annotations
      @throws( ... )
19.  final def wait(arg0: Long): Unit
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      AnyRef
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      @native() @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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