org.bdgenomics.adam.models

ReferencePosition

class ReferencePosition extends ReferenceRegion

A single genomic locus.

Linear Supertypes
ReferenceRegion, Serializable, Serializable, Product, Equals, Interval[ReferenceRegion], Comparable[ReferenceRegion], AnyRef, Any
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Inherited
  1. ReferencePosition
  2. ReferenceRegion
  3. Serializable
  4. Serializable
  5. Product
  6. Equals
  7. Interval
  8. Comparable
  9. AnyRef
  10. Any
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Instance Constructors

  1. new ReferencePosition(referenceName: String, pos: Long, strand: Strand = ...)

    referenceName

    The name of the reference contig this locus exists on.

    pos

    The position of this locus.

    strand

    The strand that this locus is on.

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. def compareTo(that: ReferenceRegion): Int

    Compares between two regions using the RegionOrdering.

    Compares between two regions using the RegionOrdering.

    that

    The region to compare against.

    returns

    An ordering depending on which region comes first.

    Definition Classes
    ReferenceRegion → Interval → Comparable
  9. def contains(other: ReferenceRegion): Boolean

    Checks if another region is wholly within our region.

    Checks if another region is wholly within our region.

    other

    The region to compare against.

    returns

    True if the region is wholly contained within our region.

    Definition Classes
    ReferenceRegion
  10. def covers(other: ReferenceRegion, threshold: Long): Boolean

    Checks if our region overlaps or is within a threshold of another region, independent of strand.

    Checks if our region overlaps or is within a threshold of another region, independent of strand.

    other

    The region to compare against.

    threshold

    The threshold within which the region must match.

    returns

    True if any section of the two regions overlap.

    Definition Classes
    ReferenceRegion
  11. def covers(other: ReferenceRegion): Boolean

    Checks if our region overlaps (wholly or partially) another region, independent of strand.

    Checks if our region overlaps (wholly or partially) another region, independent of strand.

    other

    The region to compare against.

    returns

    True if any section of the two regions overlap.

    Definition Classes
    ReferenceRegion → Interval
  12. def coversBy(other: ReferenceRegion): Option[Long]

    Returns the number of bases covering another region.

    Returns the number of bases covering another region.

    A region covers another region if it is overlapping, regardless of strand.

    other

    Region to compare against.

    returns

    Returns an option containing the number of positions of coverage between two points. If the two regions do not cover each other, we return an empty option.

    Definition Classes
    ReferenceRegion
  13. def disorient: ReferenceRegion

    returns

    Returns a copy of this reference region that is on the independent strand.

    Definition Classes
    ReferenceRegion
  14. def distance(other: ReferenceRegion): Option[Long]

    Returns the distance between this reference region and another region in the reference space.

    Returns the distance between this reference region and another region in the reference space.

    other

    Region to compare against.

    returns

    Returns an option containing the distance between two points. If the point is not in our reference space, we return an empty option.

    Definition Classes
    ReferenceRegion → Interval
    Note

    Distance here is defined as the minimum distance between any point within this region, and any point within the other region we are measuring against. If the two sets overlap, the distance will be 0. If the sets abut, the distance will be 1. Else, the distance will be greater.

  15. val end: Long

    Definition Classes
    ReferenceRegion → Interval
  16. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  17. def finalize(): Unit

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

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

    Definition Classes
    ReferenceRegion → AnyRef → Any
  20. def hull(other: ReferenceRegion): ReferenceRegion

    Creates a region corresponding to the convex hull of two regions.

    Creates a region corresponding to the convex hull of two regions. Has no preconditions about the adjacency or overlap of two regions. However, regions must be in the same reference space.

    other

    Other region to compute hull of with this region.

    returns

    The convex hull of both unions.

    Definition Classes
    ReferenceRegion
    Exceptions thrown
    IllegalArgumentException

    Thrown if regions are in different reference spaces.

    See also

    merge

  21. def intersection(other: ReferenceRegion, minOverlap: Long = 0L): ReferenceRegion

    Calculates the intersection of two reference regions given a minimum overlap.

    Calculates the intersection of two reference regions given a minimum overlap.

    other

    Region to intersect with.

    minOverlap

    Minimum overlap between the two reference regions.

    returns

    A smaller reference region

    Definition Classes
    ReferenceRegion
  22. def isAdjacent(other: ReferenceRegion): Boolean

    Returns whether two regions are adjacent.

    Returns whether two regions are adjacent.

    Adjacent regions do not overlap, but have no separation between start/end.

    other

    Region to compare against.

    returns

    True if regions are adjacent.

    Definition Classes
    ReferenceRegion
  23. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  24. def isNearby(other: ReferenceRegion, distanceThreshold: Long, requireStranded: Boolean = true): Boolean

    Returns whether two regions are nearby.

    Returns whether two regions are nearby.

    Two regions are near each other if the distance between the two is less than the user provided distanceThreshold.

    other

    Region to compare against.

    distanceThreshold

    The maximum distance of interest.

    requireStranded

    Strandedness is or is not required, true by default.

    returns

    True if regions are nearby.

    Definition Classes
    ReferenceRegion
  25. def length(): Long

    returns

    The length of this region in bases.

    Definition Classes
    ReferenceRegion
  26. def merge(other: ReferenceRegion, distanceThreshold: Long): ReferenceRegion

    Merges two reference regions that are within a threshold of each other.

    Merges two reference regions that are within a threshold of each other.

    other

    Other region to merge with this region.

    returns

    The merger of both unions.

    Definition Classes
    ReferenceRegion
    Exceptions thrown
    IllegalArgumentException

    Thrown if regions are not within the distance threshold.

    See also

    hull

  27. def merge(other: ReferenceRegion): ReferenceRegion

    Merges two reference regions that are contiguous.

    Merges two reference regions that are contiguous.

    other

    Other region to merge with this region.

    returns

    The merger of both unions.

    Definition Classes
    ReferenceRegion
    Exceptions thrown
    IllegalArgumentException

    Thrown if regions are not overlapping or adjacent.

    See also

    hull

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

    Definition Classes
    AnyRef
  29. final def notify(): Unit

    Definition Classes
    AnyRef
  30. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  31. def overlaps(other: ReferenceRegion, threshold: Long): Boolean

    Checks if our region overlaps (wholly or partially) another region.

    Checks if our region overlaps (wholly or partially) another region.

    other

    The region to compare against.

    threshold

    The threshold within which the region must match.

    returns

    True if any section of the two regions overlap.

    Definition Classes
    ReferenceRegion
  32. def overlaps(other: ReferenceRegion): Boolean

    Checks if our region overlaps or is within a threshold of another region.

    Checks if our region overlaps or is within a threshold of another region.

    other

    The region to compare against.

    returns

    True if any section of the two regions overlap.

    Definition Classes
    ReferenceRegion → Interval
  33. def overlapsBy(other: ReferenceRegion): Option[Long]

    Returns the number of bases overlapping another region.

    Returns the number of bases overlapping another region.

    other

    Region to compare against.

    returns

    Returns an option containing the number of positions of overlap between two points. If the two regions do not overlap, we return an empty option.

    Definition Classes
    ReferenceRegion
  34. def pad(byStart: Long, byEnd: Long): ReferenceRegion

    Extends the current reference region at both the start and end, but by different numbers of bases.

    Extends the current reference region at both the start and end, but by different numbers of bases.

    byStart

    The number of bases to move the start position forward by.

    byEnd

    The number of bases to move the end position back by.

    returns

    Returns a new reference region where the start and/or end have been moved.

    Definition Classes
    ReferenceRegion
  35. def pad(by: Long): ReferenceRegion

    Extends the current reference region at both the start and end.

    Extends the current reference region at both the start and end.

    by

    The number of bases to extend the region by from both the start and the end.

    returns

    Returns a new reference region where the start and end have been moved.

    Definition Classes
    ReferenceRegion
  36. val pos: Long

    The position of this locus.

  37. val referenceName: String

    The name of the reference contig this locus exists on.

    The name of the reference contig this locus exists on.

    Definition Classes
    ReferencePositionReferenceRegion
  38. final def sameReferenceName(other: ReferenceRegion): Boolean

    Determines if two regions are on the same contig.

    Determines if two regions are on the same contig.

    other

    The other region.

    returns

    True if the two are on the same reference name, false otherwise.

    Definition Classes
    ReferenceRegion
    Annotations
    @inline()
  39. final def sameStrand(other: ReferenceRegion): Boolean

    Determines if two regions are on the same strand.

    Determines if two regions are on the same strand.

    other

    The other region.

    returns

    True if the two are on the same strand, false otherwise

    Definition Classes
    ReferenceRegion
    Annotations
    @inline()
  40. val start: Long

    Definition Classes
    ReferenceRegion → Interval
  41. val strand: Strand

    The strand that this locus is on.

    The strand that this locus is on.

    Definition Classes
    ReferencePositionReferenceRegion
  42. def subtract(other: ReferenceRegion, requireStranded: Boolean = false): Iterable[ReferenceRegion]

    Subtracts another region.

    Subtracts another region.

    Subtracting in this case removes the entire region and returns up to two new regions.

    other

    The region to subtract.

    requireStranded

    Whether or not to require other be on same strand.

    returns

    A list containing the regions resulting from the subtraction.

    Definition Classes
    ReferenceRegion
  43. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  44. def toPredicate: FilterPredicate

    Generates a predicate that can be used with Parquet files.

    Generates a predicate that can be used with Parquet files.

    returns

    A predicate that selects records that overlap a given genomic region.

    Definition Classes
    ReferenceRegion
  45. def unstrandedDistance(other: ReferenceRegion): Option[Long]

    Returns the distance to another region, ignoring strand.

    Returns the distance to another region, ignoring strand.

    other

    Region to compare against.

    returns

    Returns an option containing the distance between two points. If the point is not in our reference space, we return an empty option.

    Definition Classes
    ReferenceRegion
    Note

    Distance here is defined as the minimum distance between any point within this region, and any point within the other region we are measuring against. If the two sets overlap, the distance will be 0. If the sets abut, the distance will be 1. Else, the distance will be greater.

  46. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  49. def width: Long

    Definition Classes
    Interval

Inherited from ReferenceRegion

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Interval[ReferenceRegion]

Inherited from Comparable[ReferenceRegion]

Inherited from AnyRef

Inherited from Any

Ungrouped