Overlap methods revised

marco-mariotti commented 3 months ago

I built the last (?) how-to page, about overlap-related methods, and I corrected interfaces and functioning in response. Overview of changes:

added slack to overlap
changed how strand_behavior 'opposite' is resolved in various methods
join_ranges now preserve order of left object; but resets index (otherwise, what do we put in index for 'right'/'outer' for right rows without overlap?)
count_overlaps, intersect, subtract_ranges now preserve order of left object
fixed bugs in nearest

Important: I changed the meaning for slack for consistency: now slack=0 means bookended intervals do not overlap in all methods. This required changes in max_disjoint, merge_overlaps, cluster

marco-mariotti commented 3 months ago

@endrebak I appreciate your feedback on this one, it's potentially a big change, and the last one before advertising this version

endrebak commented 3 months ago

I will have time to look at it 20. of May.

endrebak commented 3 months ago

Scratch that. I'll have to start looking at my Ph.D. then. Taking the month of June off to revise my Ph.D. and won't look at pyranges until after then.

pyranges / pyranges_1.x

Overlap methods revised #21