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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
87 stars 13 forks source link

Feature/improv param estimation minimizers #204

Closed pirovc closed 2 years ago

pirovc commented 2 years ago

Improve bin_length estimation and report true max fp and avg fp on ganon-build

removed --max-filter-size and added --faster

codecov-commenter commented 2 years ago

Codecov Report

Merging #204 (4168ad3) into dev (af00a99) will decrease coverage by 5.53%. The diff coverage is 68.25%.

@@            Coverage Diff             @@
##              dev     #204      +/-   ##
==========================================
- Coverage   77.66%   72.12%   -5.54%     
==========================================
  Files          22       14       -8     
  Lines        2512     1532     -980     
==========================================
- Hits         1951     1105     -846     
+ Misses        561      427     -134
Impacted Files Coverage Δ
...classify/hierarchical_interleaved_bloom_filter.hpp 0.00% <0.00%> (ø)
src/utils/include/utils/LCA.hpp 96.77% <ø> (ø)
src/ganon-build/include/ganon-build/Config.hpp 39.39% <30.90%> (-6.07%) :arrow_down:
...c/ganon-classify/include/ganon-classify/Config.hpp 50.61% <47.59%> (+0.61%) :arrow_up:
src/ganon-classify/GanonClassify.cpp 80.40% <77.65%> (-2.42%) :arrow_down:
src/ganon-build/GanonBuild.cpp 79.36% <78.82%> (+11.84%) :arrow_up:
src/ganon-build/CommandLineParser.cpp 88.46% <91.66%> (+0.58%) :arrow_up:
src/ganon-classify/CommandLineParser.cpp 86.66% <94.11%> (+4.61%) :arrow_up:
src/utils/include/utils/adjust_seed.hpp 100.00% <100.00%> (ø)
src/utils/include/utils/load_map.hpp 100.00% <100.00%> (ø)
... and 14 more

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