Class

org.bdgenomics.adam.util

TwoBitFile

Related Doc: package util

Permalink

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)

    Permalink

    byteAccess

    ByteAccess pointing to a .2bit file.

Value Members

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

    Permalink
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any
  5. def clone(): AnyRef

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any
  8. def extract(region: ReferenceRegion): String

    Permalink

    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

    Permalink

    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

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  11. final def getClass(): Class[_]

    Permalink
    Definition Classes
    AnyRef → Any
  12. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any
  13. var indexRecordStart: Int

    Permalink
  14. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any
  15. final def ne(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  16. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef
  17. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef
  18. val sequences: SequenceDictionary

    Permalink

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

    Permalink
    Definition Classes
    AnyRef
  20. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any
  21. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long, arg1: Int): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. final def wait(arg0: Long): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped