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Timeline / interest for not yet implemented foverlaps() functionality #3002

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sritchie73 opened this issue Aug 20, 2018 · 6 comments
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enhancement non-equi joins rolling, overlapping, non-equi joins top request One of our most-requested issues

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@sritchie73
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sritchie73 commented Aug 20, 2018

There are a number of arguments in the foverlaps() function that are not yet implemented:

Along with a few requested features:

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?

@msummersgill
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Related: #3007 foverlaps error message could be more informative

@arunsrinivasan
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@sritchie73 thanks for this. I wrote foverlaps in 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
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Atrebas commented Feb 16, 2019

Some potentially helpful other references: bedops, bedtools, tidygenomics.

@jangorecki jangorecki added the non-equi joins rolling, overlapping, non-equi joins label Apr 5, 2020
@jangorecki jangorecki removed the High label Jun 3, 2020
@Al-Murphy
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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
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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
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For those looking for not yet implemented functionality in foverlaps, please go to #528 (comment) and provide example code

@MichaelChirico MichaelChirico added the top request One of our most-requested issues label Apr 14, 2024
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Labels
enhancement non-equi joins rolling, overlapping, non-equi joins top request One of our most-requested issues
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