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BioJulia / Indexes.jl

MIT License
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Switch to CodecBGZF #5

Closed jakobnissen closed 3 years ago

jakobnissen commented 3 years ago

Pinging @CiaranOMara

I'd like to move XAM over to CodecBGZF (eventually)... but this small ecosystem around XAM is pretty hard to work with. There are no tests for this package, for example.

I'm not sure what this package is supposed to do and cover, precisely. Without tests I have no idea if this even works.

CiaranOMara commented 3 years ago

I sympathise with you when you say XAM is difficult to work with.

Indexes.jl was pulled out of GenomicFeatures.jl v1. In hindsight, Tabix.jl would have probably been a better name for this package, instead of the directory name that the original code was under.

There should certainly be tests here. In the past, the code here was covered by the eachoverlap tests of the various readers that were in GenomicFeatures.jl v1 -- in essence, it still is.

CiaranOMara commented 3 years ago

@jakobnissen, would you please rebase this PR on top of the develop branch and add version bounds for Julia.