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[MRG] allow gzipped gather csv inputs to tax #2339

Merged
merged 3 commits into from
Oct 19, 2022
Merged

[MRG] allow gzipped gather csv inputs to tax #2339

merged 3 commits into from
Oct 19, 2022

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bluegenes
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closes #2293

Uses sourmash_args.FileInputCSV context manager (introduced in #2195) to handle gather input to allow gz inputs.

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codecov bot commented Oct 19, 2022

Codecov Report

Merging #2339 (f699be2) into latest (2b86b0d) will increase coverage by 8.14%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2339      +/-   ##
==========================================
+ Coverage   84.00%   92.14%   +8.14%     
==========================================
  Files         129      100      -29     
  Lines       14967    11420    -3547     
  Branches     2192     2192              
==========================================
- Hits        12573    10523    -2050     
+ Misses       2100      603    -1497     
  Partials      294      294              
Flag Coverage Δ
python 92.14% <100.00%> (-0.01%) ⬇️
rust ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/sourmash/tax/tax_utils.py 98.32% <100.00%> (-0.01%) ⬇️
src/core/src/ffi/hyperloglog.rs
src/core/src/errors.rs
src/core/src/ffi/nodegraph.rs
src/core/src/lib.rs
src/core/src/signature.rs
src/core/src/index/mod.rs
src/core/src/sketch/hyperloglog/estimators.rs
src/core/src/ffi/utils.rs
src/core/src/ffi/index/revindex.rs
... and 20 more

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@bluegenes
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@ctb @sourmash-bio/devs ready for review

@bluegenes bluegenes merged commit d7a6fb9 into latest Oct 19, 2022
@bluegenes bluegenes deleted the gz-tax branch October 19, 2022 15:47
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Successfully merging this pull request may close these issues.

tax annotate does not support loading of gzipped gather CSVs
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