Class/Object

org.bdgenomics.adam.util

TwoBitFile

Related Docs: object TwoBitFile | package util

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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)

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    byteAccess

    ByteAccess pointing to a .2bit file.

Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. val bytes: ByteBuffer

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  6. def clone(): AnyRef

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

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

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    Definition Classes
    AnyRef

  8. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  9. def extract(region: ReferenceRegion): String

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    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

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

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    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.

  11. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  13. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  14. var indexRecordStart: Int

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  15. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  17. final def notify(): Unit

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    Definition Classes
    AnyRef

  18. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  19. val numSeq: Int

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  20. val seqRecords: Map[String, TwoBitRecord]

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  21. val sequences: SequenceDictionary

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    Definition Classes
    TwoBitFile → ReferenceFile

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

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    Definition Classes
    AnyRef

  23. def toString(): String

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    Definition Classes
    AnyRef → Any

  24. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped