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BioJulia / GenomicFeatures.jl

Tools for genomic features in Julia.
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Various julia 1.0 updates. #16

Closed dcjones closed 6 years ago

dcjones commented 6 years ago

Here's a bunch more Julia 1.0 fixes building off the work @BenJWard started in PR #15 . All tests pass under Julia 1.0 for me with this.

codecov[bot] commented 6 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (updates@b1559f6). Click here to learn what that means. The diff coverage is 98.49%.

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@@            Coverage Diff             @@
##             updates      #16   +/-   ##
==========================================
  Coverage           ?   92.33%           
==========================================
  Files              ?       32           
  Lines              ?     1369           
  Branches           ?        0           
==========================================
  Hits               ?     1264           
  Misses             ?      105           
  Partials           ?        0
Impacted Files Coverage Δ
src/intervalcollection.jl 97.1% <100%> (ø)
src/bigbed/overlap.jl 100% <100%> (ø)
src/indexes/overlap.jl 93.54% <100%> (ø)
src/coverage.jl 93.18% <100%> (ø)
src/bed/reader.jl 84.21% <100%> (ø)
src/bbi/btree.jl 96.66% <100%> (ø)
src/bigwig/overlap.jl 100% <100%> (ø)
src/bigwig/stats.jl 100% <100%> (ø)
src/overlap.jl 100% <100%> (ø)
src/bbi/rtree.jl 97.1% <100%> (ø)
... and 11 more

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TransGirlCodes commented 6 years ago

Thank you so much for this @dcjones! As you likely saw I was working on the iterators primarily as the new iterate method changes these somewhat (for the better I hope - I could certainly make some of the code more terse using Base.flatten as inspiration. Sadly, I got held up this week with the bossman comming back from paternity leave and a lot of homelife tasks. I will have a read over this later today and do a merge :)

dcjones commented 6 years ago

Yeah, some of the iterators could maybe be more idiomatic. I mostly just adapted the existing ones, except for OverlapIterator, which I had to reimplement.

TransGirlCodes commented 6 years ago

That's the one that applies to streams right? IIRC I has just about finished modding the stream vs collection overlap iterator and was thinking "Oh boy, I should to the streamed one this weekend", but this looks great :) I'll merge this now.

dcjones commented 6 years ago

Thanks! I'll get to work on BioAlignments next. :v: