XAM cannot install with GenomicFeatures v3.0.0

[SeqCrafter]

XAM cannot install with GenomicFeatures v3.0.0.

[kescobo]

Incidentally, it seems crazy that we don't have v1 for Xam yet...

[mzdravkov]

Hi! I stumbled the same issue and I thought that maybe I can try to fix it and open a pull request, but the problem is more hairy than I thought at first.

Initially, I was thinking that since XAM has quite minimal dependency on GenomicFeatures (as far as I can see it's just the renaming of Interval to GenomicInterval in GenomicFeatures that would be an issue) I could get it to support both versions with an alias. For example I tried adding something like this in src/bam/bam.jl:

# Version 3 of GenomicFeatures renamed Interval to
# GenomicInterval. If GenomicInterval is not defined
# then a legacy pre-v3 version of GenomicFeatures is
# being used.
if !isdefined(GenomicFeatures, :GenomicInterval)
    if isdefined(GenomicFeatures, :Interval)
        const GenomicInterval = GenomicFeatures.Interval
    else
        # This shouldn't really happen, unless backwards
        # incopmatible changes were introduced in GenomicFeatures.
        error("The GenomicFeatures package defines neither Interval nor GenomicInterval.")
    end
end

# Then use the GenomicInterval alias throughout the package,
# which would be either the true type of v3 or an alias to Interval in v2.

However, the problem is repeated across the whole tree of packages depending on GenomicFeatures, e.g. XAM depends on Indexes whose latest version is still pinned to GenomicFeatures v2. So I don't think that such a workaround as the one above would be clean and work nicely. So I guess the alternative is to make a backwards incompatible change to each package that depends on GenomicFeatures to change it to v3. Are there any plans for doing this?

[kescobo]

@jakobnissen Do we have an existing plan to synchronize these changes?