class ReferencePosition extends ReferenceRegion
A single genomic locus.
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- ReferenceRegion
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Instance Constructors
-
new
ReferencePosition(referenceName: String, pos: Long, strand: Strand = Strand.INDEPENDENT)
- referenceName
The name of the reference sequence this locus exists on.
- pos
The position of this locus.
- strand
The strand that this locus is on.
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
- Attributes
- protected[lang]
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- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
-
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
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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
-
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
-
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
-
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
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def
disorient: ReferenceRegion
- returns
Returns a copy of this reference region that is on the independent strand.
- Definition Classes
- ReferenceRegion
-
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.
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val
end: Long
- Definition Classes
- ReferenceRegion → Interval
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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final
def
getClass(): Class[_]
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- @native() @HotSpotIntrinsicCandidate()
-
def
hashCode(): Int
- Definition Classes
- ReferenceRegion → AnyRef → Any
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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
-
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
-
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
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
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
-
def
length(): Long
- returns
The length of this region in bases.
- Definition Classes
- ReferenceRegion
-
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
-
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
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
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- @native() @HotSpotIntrinsicCandidate()
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final
def
notifyAll(): Unit
- Definition Classes
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- @native() @HotSpotIntrinsicCandidate()
-
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
-
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
-
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
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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
-
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
- val pos: Long
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val
referenceName: String
- Definition Classes
- ReferencePosition → ReferenceRegion
-
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.
- Definition Classes
- ReferenceRegion
- Annotations
- @inline()
-
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()
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val
start: Long
- Definition Classes
- ReferenceRegion → Interval
-
val
strand: Strand
- Definition Classes
- ReferencePosition → ReferenceRegion
-
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
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
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
-
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.
-
final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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final
def
wait(): Unit
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def
width: Long
- Definition Classes
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Deprecated Value Members
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def
finalize(): Unit
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(Since version ) see corresponding Javadoc for more information.