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https://github.com/bmdavid2/OligoRL/pull/1
seems to be the canary in the coalmine for a larger issue.
BioSequences
seems to have changed `LongDNASeq` -> `LongDNA`
as per
https://github.com/BioJul…
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The notebooks as they stand are from Julia 0.5
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revisiting a (5 yro :) conversation about interoperability https://github.com/marbl/Mash/issues/27 after some discussions on slack with @kescobo on [µbioinfo slack](https://microbial-bioinfo.slack.com…
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See https://github.com/BioJulia/Libz.jl/issues/68
Libz.jl is no longer maintained, and now recommends folks use CodecZlib instead. In any case, the implementation for Libz.jl is no longer functiona…
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Just found this repo, but I notice that there are only two commits, the last of which was in 2015. Is this project still alive?
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MWE:
```
CodecBGZF.jl on master via C base took 18s ❯ julia --project=. --startup-file=no -q -t 3
julia> using CodecBGZF
julia> open("/tmp/foo.bgz", "w") do file
io = BGZFCompresso…
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While I was benchmarking Julia's `pairalign` (318 μs) against BioPython (7310 µs) and scikit-bio (925 µs) implementation, I found that Julia's local alignment returns a solution with score 63 while py…
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Right now, most julia packages making use of these files do so using something like this (taken [from here](https://github.com/BioJulia/BioSequences.jl/blob/master/test/runtests.jl#L46-L51))
```
f…
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* Make SAM and BAM records display similarly
A SAM and BAM record contain basically the same information. So they should be displayed similarly in the REPL.
* Create SAM-to-BAM conversion function…
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http://en.wikipedia.org/wiki/Allen%27s_interval_algebra