org.bdgenomics.adam.util

# ReferenceFile

###
Related Doc: package util

#### 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
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. ReferenceFile
2. Serializable
3. Serializable
4. AnyRef
5. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### 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

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

   Definition Classes
     AnyRef

7. #### def equals(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

8. #### def finalize(): Unit

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

9. #### final def getClass(): Class[_]

   Definition Classes
     AnyRef → Any

10. #### def hashCode(): Int

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

    Definition Classes
      AnyRef

16. #### def toString(): String

    Definition Classes
      AnyRef → Any

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 Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped