bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
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Change support for MAVIS input in summary module #336

Closed zhemingfan closed 1 year ago

zhemingfan commented 1 year ago

Addresses issues in https://github.com/bcgsc/mavis/issues/307

codecov[bot] commented 1 year ago

Codecov Report

Base: 86.81% // Head: 86.92% // Increases project coverage by +0.10% :tada:

Coverage data is based on head (bfdf8b7) compared to base (ec82b70). Patch coverage: 95.94% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop_v3 #336 +/- ## ============================================== + Coverage 86.81% 86.92% +0.10% ============================================== Files 57 57 Lines 9327 9390 +63 Branches 2335 2355 +20 ============================================== + Hits 8097 8162 +65 + Misses 755 752 -3 - Partials 475 476 +1 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `86.92% <95.94%> (+0.10%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/bcgsc/mavis/pull/336?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc) | Coverage Δ | | |---|---|---| | [src/mavis/summary/main.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL3N1bW1hcnkvbWFpbi5weQ==) | `77.30% <ø> (ø)` | | | [src/mavis/summary/summary.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL3N1bW1hcnkvc3VtbWFyeS5weQ==) | `70.00% <93.18%> (+5.41%)` | :arrow_up: | | [src/mavis/annotate/file\_io.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL2Fubm90YXRlL2ZpbGVfaW8ucHk=) | `77.06% <100.00%> (+0.65%)` | :arrow_up: | | [src/mavis/constants.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL2NvbnN0YW50cy5weQ==) | `96.72% <100.00%> (+0.02%)` | :arrow_up: | | [src/mavis/pairing/pairing.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL3BhaXJpbmcvcGFpcmluZy5weQ==) | `89.86% <100.00%> (+0.13%)` | :arrow_up: | | [src/mavis/util.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL3V0aWwucHk=) | `80.07% <0.00%> (+1.42%)` | :arrow_up: | | [src/mavis/cluster/cluster.py](https://codecov.io/gh/bcgsc/mavis/pull/336/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-c3JjL21hdmlzL2NsdXN0ZXIvY2x1c3Rlci5weQ==) | `92.10% <0.00%> (+2.63%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc)

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zhemingfan commented 1 year ago

The version of tabulate has been frozen to version 0.8.9 according to the fix suggested in the Snakemake repository.

creisle commented 1 year ago

Can you also add a description of the new column here? docs/outputs/columns.md

zhemingfan commented 1 year ago

Can you also add a description of the new column here? docs/outputs/columns.md

Added column information in the columns 960bd67.