ReferenceRegion
Related Docs:
object ReferenceRegion
| package models
The name of the sequence (chromosome) in the reference genome
The 0-based residue-coordinate for the start of the region
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.
The strand of the genome that this region exists on.
Compares between two regions using the RegionOrdering.
Compares between two regions using the RegionOrdering.
The region to compare against.
An ordering depending on which region comes first.
Checks if another region is wholly within our region.
Checks if another region is wholly within our region.
The region to compare against.
True if the region is wholly contained within our region.
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.
The region to compare against.
The threshold within which the region must match.
True if any section of the two regions overlap.
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.
The region to compare against.
True if any section of the two regions overlap.
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.
Region to compare against.
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.
Returns a copy of this reference region that is on the independent strand.
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.
Region to compare against.
Returns an option containing the distance between two points. If the point is not in our reference space, we return an empty option.
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.
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.
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 region to compute hull of with this region.
The convex hull of both unions.
IllegalArgumentException Thrown if regions are in different reference spaces.
merge
Calculates the intersection of two reference regions given a minimum overlap.
Calculates the intersection of two reference regions given a minimum overlap.
Region to intersect with.
Minimum overlap between the two reference regions.
A smaller reference region
Returns whether two regions are adjacent.
Returns whether two regions are adjacent.
Adjacent regions do not overlap, but have no separation between start/end.
Region to compare against.
True if regions are adjacent.
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.
Region to compare against.
The maximum distance of interest.
Strandedness is or is not required, true by default.
True if regions are nearby.
The length of this region in bases.
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 region to merge with this region.
The merger of both unions.
IllegalArgumentException Thrown if regions are not within the
distance threshold.
hull
Merges two reference regions that are contiguous.
Merges two reference regions that are contiguous.
Other region to merge with this region.
The merger of both unions.
IllegalArgumentException Thrown if regions are not overlapping or adjacent.
hull
Checks if our region overlaps (wholly or partially) another region.
Checks if our region overlaps (wholly or partially) another region.
The region to compare against.
The threshold within which the region must match.
True if any section of the two regions overlap.
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.
The region to compare against.
True if any section of the two regions overlap.
Returns the number of bases overlapping another region.
Returns the number of bases overlapping another region.
Region to compare against.
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.
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.
The number of bases to move the start position forward by.
The number of bases to move the end position back by.
Returns a new reference region where the start and/or end have been moved.
Extends the current reference region at both the start and end.
Extends the current reference region at both the start and end.
The number of bases to extend the region by from both the start and the end.
Returns a new reference region where the start and end have been moved.
The name of the sequence (chromosome) in the reference genome
Determines if two regions are on the same contig.
Determines if two regions are on the same contig.
The other region.
True if the two are on the same reference name, false otherwise.
Determines if two regions are on the same strand.
Determines if two regions are on the same strand.
The other region.
True if the two are on the same strand, false otherwise
The 0-based residue-coordinate for the start of the region
The 0-based residue-coordinate for the start of the region
The strand of the genome that this region exists on.
Subtracts another region.
Subtracts another region.
Subtracting in this case removes the entire region and returns up to two new regions.
The region to subtract.
Whether or not to require other be on same strand.
A list containing the regions resulting from the subtraction.
Generates a predicate that can be used with Parquet files.
Generates a predicate that can be used with Parquet files.
A predicate that selects records that overlap a given genomic region.
Returns the distance to another region, ignoring strand.
Returns the distance to another region, ignoring strand.
Region to compare against.
Returns an option containing the distance between two points. If the point is not in our reference space, we return an empty option.
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.
Represents a contiguous region of the reference genome.
The name of the sequence (chromosome) in the reference genome
The 0-based residue-coordinate for the start of the region
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.
The strand of the genome that this region exists on.