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Timeline / interest for not yet implemented foverlaps() functionality #3002
Description
There are a number of arguments in the foverlaps() function that are not yet implemented:
-
type = "equal"- [FR] foverlaps type="equal" implementation #3416 -
maxgap -
minoverlap
Along with a few requested features:
- non-integer value support for minoverlap argument of foverlaps function #979 non integer support for
minoverlap - foverlaps() should work without having to set keys #1355
foverlaps()should work withoutsetkey()beforehand - Return length of overlap in foverlaps #1975 return length of overlap
- foverlaps throws cryptic error when provided factors #2645
foverlaps()could work with factor levels
There will be a lesson on the foverlaps() function in the DataCamp course on joins, so I'm wanting to gauge whether its worth trying to implement these features before the course is released. Are there obvious technical barriers that have prevented these features from being implemented? Or has there been a lack of interest from the community and developers, e.g. given the availability of GenomicRanges?
Activity
msummersgill commentedon Aug 21, 2018
Related: #3007 foverlaps error message could be more informative
arunsrinivasan commentedon Feb 16, 2019
@sritchie73 thanks for this. I wrote
foverlapsin about 3-4 hrs (for EARL conference) and have not since looked at the features that've been left out .. Will take a look.Atrebas commentedon Feb 16, 2019
Some potentially helpful other references: bedops, bedtools, tidygenomics.
Al-Murphy commentedon Oct 1, 2021
Hi, just wondering if maxgap, minoverlap is likely to be implemented soon? I think it would be a brilliant addition to avoid the conversion to GRanges object.
MichaelChirico commentedon Oct 4, 2021
Hey @Al-Murphy that's definitely in "contributions welcome" status... happy to support however I can if you wanted to take up the gauntlet 😃
cc @arunsrinivasan who would be most familiar with that part of the code base & maybe better able to offer "mentor" support (not sure availability)
jangorecki commentedon Jan 7, 2024
For those looking for not yet implemented functionality in foverlaps, please go to #528 (comment) and provide example code