BioJulia / FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.
https://biojulia.dev
MIT License
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Use SIMD code generator #42

Closed jakobnissen closed 2 years ago

jakobnissen commented 3 years ago

This PR is only compatible with https://github.com/BioJulia/Automa.jl/pull/60 - so it can't be merged yet. I'm ambivalent as to whether this should be merged at all.

See that PR for the pros/cons

codecov[bot] commented 3 years ago

Codecov Report

Merging #42 (79dd2c2) into release-2 (e9202ba) will decrease coverage by 2.94%. The diff coverage is 0.00%.

Impacted file tree graph

@@              Coverage Diff              @@
##           release-2      #42      +/-   ##
=============================================
- Coverage      83.57%   80.63%   -2.95%     
=============================================
  Files             11       12       +1     
  Lines            615      661      +46     
=============================================
+ Hits             514      533      +19     
- Misses           101      128      +27     
Flag Coverage Δ
unittests 80.63% <0.00%> (-2.95%) :arrow_down:

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Impacted Files Coverage Δ
src/fasta/readrecord.jl 96.42% <ø> (ø)
src/fastq/readrecord.jl 46.15% <0.00%> (ø)
src/fasta/record.jl 65.24% <0.00%> (-15.05%) :arrow_down:
src/fastq/reader.jl 89.36% <0.00%> (-1.12%) :arrow_down:
src/fastq/record.jl 82.39% <0.00%> (-1.07%) :arrow_down:
src/fasta/reader.jl 89.85% <0.00%> (-0.63%) :arrow_down:
src/fasta/index.jl 100.00% <0.00%> (ø)
src/FASTX.jl 100.00% <0.00%> (ø)
src/fastq/writer.jl 96.77% <0.00%> (+0.22%) :arrow_up:
... and 2 more

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jakobnissen commented 2 years ago

Okay, here is what need to happen before I am comfortable merging this:

jakobnissen commented 2 years ago

This will be made obsolete with Automa v1, which will hopefully land in a few months at most