org.bdgenomics.adam.models

# ReferenceRegion

###
Related Docs: object ReferenceRegion | package models

#### case class ReferenceRegion(referenceName: String, start: Long, end: Long, strand: Strand = Strand.INDEPENDENT) extends Comparable[ReferenceRegion] with Interval[ReferenceRegion] with Product with Serializable

Represents a contiguous region of the reference genome.

referenceName

  The name of the sequence (chromosome) in the reference genome

start

  The 0-based residue-coordinate for the start of the region

end

  The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.

strand

  The strand of the genome that this region exists on.

Linear Supertypes
Serializable, Serializable, Product, Equals, Interval[ReferenceRegion], Comparable[ReferenceRegion], AnyRef, Any
Known Subclasses
ReferencePosition
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Inherited

1. ReferenceRegion
2. Serializable
3. Serializable
4. Product
5. Equals
6. Interval
7. Comparable
8. AnyRef
9. Any

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Visibility

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### Instance Constructors

1. #### new ReferenceRegion(referenceName: String, start: Long, end: Long, strand: Strand = Strand.INDEPENDENT)

   referenceName

     The name of the sequence (chromosome) in the reference genome

   start

     The 0-based residue-coordinate for the start of the region

   end

     The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.

   strand

     The strand of the genome that this region exists on.

### Value Members

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

   Definition Classes
     AnyRef → Any

2. #### final def ##(): Int

   Definition Classes
     AnyRef → Any

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

   Definition Classes
     AnyRef → Any

4. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

5. #### def clone(): AnyRef

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

6. #### 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

7. #### 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.

8. #### 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.

9. #### 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

10. #### 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.

11. #### def disorient: ReferenceRegion

    returns

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

12. #### 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.

13. #### val end: Long

    The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e.

    The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.

    Definition Classes
      ReferenceRegion → Interval

14. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

15. #### def finalize(): Unit

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

16. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

17. #### def hashCode(): Int

    Definition Classes
      ReferenceRegion → AnyRef → Any

18. #### 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.

    Exceptions thrown

      `IllegalArgumentException` Thrown if regions are in different reference spaces.

    See also

      merge

19. #### 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

20. #### 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.

21. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

22. #### 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.

23. #### def length(): Long

    returns

      The length of this region in bases.

24. #### 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.

    Exceptions thrown

      `IllegalArgumentException` Thrown if regions are not within the distance threshold.

    See also

      hull

25. #### 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.

    Exceptions thrown

      `IllegalArgumentException` Thrown if regions are not overlapping or adjacent.

    See also

      hull

26. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

27. #### final def notify(): Unit

    Definition Classes
      AnyRef

28. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

29. #### 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.

30. #### 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

31. #### 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.

32. #### 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.

33. #### 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.

34. #### val referenceName: String

    The name of the sequence (chromosome) in the reference genome

35. #### final def sameReferenceName(other: ReferenceRegion): Boolean

    Determines if two regions are on the same reference sequence.

    Determines if two regions are on the same reference sequence.

    other

      The other region.

    returns

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

    Annotations
      @inline()

36. #### 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

    Annotations
      @inline()

37. #### val start: Long

    The 0-based residue-coordinate for the start of the region

    The 0-based residue-coordinate for the start of the region

    Definition Classes
      ReferenceRegion → Interval

38. #### val strand: Strand

    The strand of the genome that this region exists on.

39. #### 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.

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

    Definition Classes
      AnyRef

41. #### 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.

42. #### 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.

    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.

43. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

45. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

46. #### def width: Long

    Definition Classes
      Interval

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from Interval[ReferenceRegion]

### Inherited from Comparable[ReferenceRegion]

### Inherited from AnyRef

### Inherited from Any

### Ungrouped