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.
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 a position is wholly within our region.
Checks if a position is wholly within our region.
The reference position to compare against.
True if the position is within our region.
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.
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.
Thrown if regions are in different reference spaces.
merge
Calculates the intersection of two reference regions.
Calculates the intersection of two reference regions.
Region to intersect with.
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.
The length of this region in bases.
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.
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.
True if any section of the two regions overlap.
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
The 0-based residue-coordinate for the start of the region
The 0-based residue-coordinate for the start of the region
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.