nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
159 stars 49 forks source link

Upgrade to using ska2 #383

Closed nickjcroucher closed 10 months ago

codecov[bot] commented 10 months ago

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.15% :warning:

Comparison is base (97f24cd) 91.13% compared to head (1b689a7) 90.99%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #383 +/- ## ========================================== - Coverage 91.13% 90.99% -0.15% ========================================== Files 45 45 Lines 5776 5795 +19 ========================================== + Hits 5264 5273 +9 - Misses 512 522 +10 ``` | [Files Changed](https://app.codecov.io/gh/nickjcroucher/gubbins/pull/383?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [python/gubbins/tests/test\_python\_scripts.py](https://app.codecov.io/gh/nickjcroucher/gubbins/pull/383?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-cHl0aG9uL2d1YmJpbnMvdGVzdHMvdGVzdF9weXRob25fc2NyaXB0cy5weQ==) | `92.30% <100.00%> (-4.78%)` | :arrow_down: | | [src/main.c](https://app.codecov.io/gh/nickjcroucher/gubbins/pull/383?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL21haW4uYw==) | `70.11% <100.00%> (ø)` | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/nickjcroucher/gubbins/pull/383/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None)

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nickjcroucher commented 10 months ago

Upgrades ska2 mapping and adds plotting script.