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.

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ReferenceFile, Serializable, Serializable, AnyRef, Any
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  1. TwoBitFile
  2. ReferenceFile
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Instance Constructors

  1. new TwoBitFile(byteAccess: ByteAccess)

    byteAccess

    ByteAccess pointing to a .2bit file.

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  10. def extract(region: ReferenceRegion): String

    Extract reference sequence from the .

    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

  11. def extract(region: ReferenceRegion, mask: Boolean): String

    Extract reference sequence from the .

    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.

  12. def finalize(): Unit

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

  13. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  14. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  15. var indexRecordStart: Int

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  17. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  18. final def notify(): Unit

    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  20. val sequences: SequenceDictionary

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

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

    Definition Classes
    TwoBitFile → ReferenceFile

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

    Definition Classes
    AnyRef

  22. def toString(): String

    Definition Classes
    AnyRef → Any

  23. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  24. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  25. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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