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bihealth / auto-acmg

Automatic classification of sequence variants and CNVs according to ACMG criteria.
GNU General Public License v3.0
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Restructure module in order to support other acmg rules #83

Closed gromdimon closed 6 months ago

gromdimon commented 6 months ago

Issue:

Description:

codecov[bot] commented 6 months ago

Codecov Report

Attention: Patch coverage is 61.36364% with 34 lines in your changes are missing coverage. Please review.

Project coverage is 78.81%. Comparing base (f85ce59) to head (f6268b2).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #83 +/- ## ========================================== + Coverage 75.50% 78.81% +3.31% ========================================== Files 17 17 Lines 1241 1232 -9 ========================================== + Hits 937 971 +34 + Misses 304 261 -43 ``` | [Files](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth) | Coverage Δ | | |---|---|---| | [src/cli.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?src=pr&el=tree&filepath=src%2Fcli.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NsaS5weQ==) | `95.45% <100.00%> (+0.21%)` | :arrow_up: | | [src/defs/seqvar.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?src=pr&el=tree&filepath=src%2Fdefs%2Fseqvar.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvc2VxdmFyLnB5) | `78.49% <83.33%> (-14.61%)` | :arrow_down: | | [src/pvs1/auto\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?src=pr&el=tree&filepath=src%2Fpvs1%2Fauto_pvs1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3B2czEvYXV0b19wdnMxLnB5) | `87.17% <80.00%> (ø)` | | | [src/defs/strucvar.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?src=pr&el=tree&filepath=src%2Fdefs%2Fstrucvar.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvc3RydWN2YXIucHk=) | `90.62% <42.85%> (-5.87%)` | :arrow_down: | | [src/auto\_acmg.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?src=pr&el=tree&filepath=src%2Fauto_acmg.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2F1dG9fYWNtZy5weQ==) | `66.21% <60.60%> (+66.21%)` | :arrow_up: | | [src/pvs1/seqvar\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83?src=pr&el=tree&filepath=src%2Fpvs1%2Fseqvar_pvs1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3B2czEvc2VxdmFyX3B2czEucHk=) | `56.53% <43.47%> (ø)` | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/bihealth/auto-acmg/pull/83/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth)