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/raptor symbolic link overwrite #279

Closed pirovc closed 7 months ago

pirovc commented 7 months ago

as reported #274 and #275

codecov-commenter commented 7 months ago

Codecov Report

Attention: 327 lines in your changes are missing coverage. Please review.

Comparison is base (af00a99) 77.66% compared to head (34d8ed5) 88.68%. Report is 123 commits behind head on dev.

:exclamation: Current head 34d8ed5 differs from pull request most recent head bd60b0f. Consider uploading reports for the commit bd60b0f to get more accurate results

Files Patch % Lines
src/ganon/build_update.py 77.01% 77 Missing :warning:
src/ganon/config.py 83.56% 60 Missing :warning:
src/ganon/tax_util.py 80.08% 48 Missing :warning:
src/ganon/report.py 90.90% 30 Missing :warning:
src/ganon-build/GanonBuild.cpp 94.85% 21 Missing :warning:
src/ganon-build/include/ganon-build/Config.hpp 61.11% 21 Missing :warning:
...c/ganon-classify/include/ganon-classify/Config.hpp 75.58% 21 Missing :warning:
src/ganon-classify/GanonClassify.cpp 95.70% 20 Missing :warning:
src/ganon/reassign.py 95.31% 6 Missing :warning:
src/ganon/util.py 93.90% 5 Missing :warning:
... and 6 more

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #279 +/- ## =========================================== + Coverage 77.66% 88.68% +11.01% =========================================== Files 22 23 +1 Lines 2512 3516 +1004 =========================================== + Hits 1951 3118 +1167 + Misses 561 398 -163 ```

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