NonoverlappingRegions
The input-set of regions.
A quick filter, to find out if we even need to examine a particular input value for keying by nonoverlapping-regions.
A quick filter, to find out if we even need to examine a particular input value for keying by nonoverlapping-regions. Basically, reject the input value if its corresponding region is completely outside the hull of all the input-set regions.
The input value
a boolean -- the input value should only participate in the regionJoin if the return value here is 'true'.
Given a "regionable" value (corresponds to a ReferencRegion through an implicit ReferenceMapping), return the set of nonoverlapping-regions to be used as partitions for the input value in a region-join.
Given a "regionable" value (corresponds to a ReferencRegion through an implicit ReferenceMapping), return the set of nonoverlapping-regions to be used as partitions for the input value in a region-join. Basically, return the set of any non-empty nonoverlapping-regions that overlap the region corresponding to this input.
The type of the input
The input, which corresponds to a region
An Iterable[ReferenceRegion], where each element of the Iterable is a nonoverlapping-region defined by 1 or more input-set regions.
The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome. NonoverlappingRegions is a class to compute the value of that partition, and to allow us to assign one or more elements of that partition to a new ReferenceRegion (see the 'regionsFor' method).
NonoverlappingRegions takes, as input, and 'input-set' of regions. These are arbitrary ReferenceRegions, which may be overlapping, identical, disjoint, etc. The input-set of regions _must_ all be located on the same reference chromosome (i.e. must all have the same refName); the generalization to reference regions from multiple chromosomes is in MultiContigNonoverlappingRegions, below.
NonoverlappingRegions produces, internally, a 'nonoverlapping-set' of regions. This is basically the set of _distinct unions_ of the input-set regions.