ADAM_2.12: Core 0.29.0 API < Back
 

# 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

c

org.bdgenomics.adam.util

# TwoBitFile 

###

#### class TwoBitFile extends ReferenceFile

Represents a set of reference sequences backed by a .2bit file.

See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 for the spec.

Linear Supertypes
ReferenceFile, Serializable, Serializable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

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

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Instance Constructors

1.  new TwoBitFile(byteAccess: ByteAccess)

   byteAccess

     ByteAccess pointing to a .2bit file.

### 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
     @native() @throws( ... )
6.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
7.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
8.  def extract(region: ReferenceRegion): String

   Extract reference sequence from the .2bit data.

   Extract reference sequence from the .2bit data. Do not apply masks.

   region

     The desired ReferenceRegion to extract.

   returns

     The reference sequence at the desired locus.

   Definition Classes
     TwoBitFile → ReferenceFile
9.  def extract(region: ReferenceRegion, mask: Boolean): String

   Extract reference sequence from the .2bit data.

   Extract reference sequence from the .2bit data.

   region

     The desired ReferenceRegion to extract.

   mask

     Whether to apply masks (with lowercase letters)

   returns

     The reference sequence at the desired locus.

10.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
11.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
12.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
13.  var indexRecordStart: Int
14.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
15.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
16.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
17.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
18.  val sequences: SequenceDictionary

    The sequence dictionary corresponding to the reference sequences in this two bit file.

    The sequence dictionary corresponding to the reference sequences in this two bit file.

    Definition Classes
      TwoBitFile → ReferenceFile
19.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
20.  def toString(): String
    Definition Classes
      AnyRef → Any
21.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
22.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
23.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )

### Inherited from ReferenceFile

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped