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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/dna5 to dna4 #201

Closed pirovc closed 2 years ago

pirovc commented 2 years ago

use seqan3 dna4 instead of dna5. It makes indices created before incompatible.

codecov-commenter commented 2 years ago

Codecov Report

Merging #201 (4301f65) into dev (af00a99) will decrease coverage by 2.79%. The diff coverage is 72.07%.

@@            Coverage Diff             @@
##              dev     #201      +/-   ##
==========================================
- Coverage   77.66%   74.87%   -2.80%     
==========================================
  Files          22       11      -11     
  Lines        2512     1373    -1139     
==========================================
- Hits         1951     1028     -923     
+ Misses        561      345     -216
Impacted Files Coverage Δ
src/utils/include/utils/LCA.hpp 96.77% <ø> (ø)
src/ganon-build/include/ganon-build/Config.hpp 40.20% <32.69%> (-5.25%) :arrow_down:
...c/ganon-classify/include/ganon-classify/Config.hpp 50.82% <47.87%> (+0.82%) :arrow_up:
src/ganon-build/GanonBuild.cpp 78.70% <78.15%> (+11.18%) :arrow_up:
src/ganon-classify/GanonClassify.cpp 83.93% <82.47%> (+1.11%) :arrow_up:
src/ganon-build/CommandLineParser.cpp 88.00% <90.47%> (+0.12%) :arrow_up:
src/ganon-classify/CommandLineParser.cpp 87.35% <96.77%> (+5.30%) :arrow_up:
src/ganon/bins.py
src/ganon/build_update.py
src/ganon/classify.py
... and 11 more

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