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
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Inherited
  1. TwoBitFile
  2. ReferenceFile
  3. Serializable
  4. Serializable
  5. AnyRef
  6. Any
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Visibility
  1. Public
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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[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  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
    TwoBitFileReferenceFile
  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[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 references: 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
    TwoBitFileReferenceFile
  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
    @throws( ... ) @native()

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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