Class

org.hammerlab.genomics.reference

Slice

Related Doc: package reference

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case class Slice(contigName: ContigName, start: Locus, bases: Bases) extends Region with Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, Region, Interval, HasContig, AnyRef, Any
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Inherited
  1. Slice
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Region
  7. Interval
  8. HasContig
  9. AnyRef
  10. Any
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Visibility
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Instance Constructors

  1. new Slice(contigName: ContigName, start: Locus, bases: Bases)

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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. def apply(locus: Locus): Byte

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  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  6. val bases: Bases

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  7. def clone(): AnyRef

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

  8. def contains(locus: Locus): Boolean

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    Definition Classes
    Interval

  9. val contigName: ContigName

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    Definition Classes
    Slice → HasContig

  10. val end: Locus

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    0-based end position on a contig.

    0-based end position on a contig.

    Definition Classes
    Slice → Interval

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

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    Definition Classes
    AnyRef

  12. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  15. def iterator(): Iterator[Locus]

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    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes
    Interval

  16. def length: NumLoci

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    Number of elements in the range.

    Number of elements in the range.

    Definition Classes
    Interval

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

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    Definition Classes
    AnyRef

  18. final def notify(): Unit

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    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  20. def overlaps(other: Region): Boolean

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    Does the region overlap another reference region

    Does the region overlap another reference region

    other

    another region on the genome

    returns

    True if the the regions overlap

    Definition Classes
    Region

  21. def overlapsLocus(locus: Locus, halfWindowSize: WindowSize = 0): Boolean

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    Does the region overlap the given locus, with halfWindowSize padding?

    Does the region overlap the given locus, with halfWindowSize padding?

    Definition Classes
    Region

  22. def slice(sliceStart: Locus, sliceEnd: Locus = end): Seq[Byte]

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  23. val start: Locus

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    0-based start position on a contig.

    0-based start position on a contig.

    Definition Classes
    Slice → Interval

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

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    Definition Classes
    AnyRef

  25. def toString(): String

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    Definition Classes
    Region → Interval → Any

  26. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Region

Inherited from Interval

Inherited from HasContig

Inherited from AnyRef

Inherited from Any

Ungrouped