pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
86 stars 13 forks source link

Feature/hibf raptor integration #235

Closed pirovc closed 1 year ago

pirovc commented 1 year ago

Integrated HIBF build (calling raptor) on ganon build and update the classification to HIBFs generated by raptor v3

codecov-commenter commented 1 year ago

Codecov Report

Merging #235 (6e6ab04) into dev (af00a99) will increase coverage by 9.03%. The diff coverage is 86.40%.

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@@            Coverage Diff             @@
##              dev     #235      +/-   ##
==========================================
+ Coverage   77.66%   86.70%   +9.03%     
==========================================
  Files          22       22              
  Lines        2512     3098     +586     
==========================================
+ Hits         1951     2686     +735     
+ Misses        561      412     -149     
Impacted Files Coverage Δ
...classify/hierarchical_interleaved_bloom_filter.hpp 0.00% <0.00%> (ø)
src/utils/include/utils/LCA.hpp 96.92% <ø> (+0.14%) :arrow_up:
src/ganon-build/include/ganon-build/Config.hpp 64.51% <60.37%> (+19.06%) :arrow_up:
...c/ganon-classify/include/ganon-classify/Config.hpp 70.00% <77.94%> (+20.00%) :arrow_up:
src/ganon/classify.py 83.33% <80.00%> (-10.79%) :arrow_down:
src/ganon/tax_util.py 81.25% <81.25%> (ø)
src/ganon/config.py 78.59% <82.50%> (+0.63%) :arrow_up:
src/ganon/build_update.py 83.54% <83.55%> (+18.06%) :arrow_up:
src/ganon/ganon.py 87.87% <86.36%> (-6.07%) :arrow_down:
src/ganon-classify/GanonClassify.cpp 90.73% <87.69%> (+7.91%) :arrow_up:
... and 20 more

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