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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

Bugfix/multi db kmer window params #190

Closed pirovc closed 2 years ago

pirovc commented 2 years ago

fix #189

--window-size and --kmer-size are now passed by hierarchy level, not by database from the wrapper to cpp.

codecov-commenter commented 2 years ago

Codecov Report

Merging #190 (e5d7489) into dev (af00a99) will decrease coverage by 2.83%. The diff coverage is 72.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #190      +/-   ##
==========================================
- Coverage   77.66%   74.83%   -2.84%     
==========================================
  Files          22       11      -11     
  Lines        2512     1371    -1141     
==========================================
- Hits         1951     1026     -925     
+ 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 83.86% <82.37%> (+1.04%) :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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