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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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Adapt pydantic models #150

Closed gromdimon closed 1 month ago

gromdimon commented 1 month ago

Issue:

Description:

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 21.17647% with 67 lines in your changes missing coverage. Please review.

Project coverage is 50.38%. Comparing base (2373b0f) to head (c10fe13).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #150 +/- ## ========================================== + Coverage 50.25% 50.38% +0.13% ========================================== Files 35 35 Lines 3397 3398 +1 ========================================== + Hits 1707 1712 +5 + Misses 1690 1686 -4 ``` | [Files](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?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/criteria/auto\_pm4\_bp3.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_pm4_bp3.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fcG00X2JwMy5weQ==) | `28.81% <ø> (+0.94%)` | :arrow_up: | | [src/defs/annonars\_range.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fdefs%2Fannonars_range.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvYW5ub25hcnNfcmFuZ2UucHk=) | `100.00% <100.00%> (ø)` | | | [src/defs/annonars\_variant.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fdefs%2Fannonars_variant.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvYW5ub25hcnNfdmFyaWFudC5weQ==) | `100.00% <100.00%> (ø)` | | | [src/defs/auto\_acmg.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fdefs%2Fauto_acmg.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvYXV0b19hY21nLnB5) | `95.56% <ø> (ø)` | | | [src/criteria/auto\_ps1\_pm5.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_ps1_pm5.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fcHMxX3BtNS5weQ==) | `55.68% <0.00%> (ø)` | | | [src/pvs1/seqvar\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?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=) | `51.55% <66.66%> (+0.44%)` | :arrow_up: | | [src/bench/comparison\_v3.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fbench%2Fcomparison_v3.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2JlbmNoL2NvbXBhcmlzb25fdjMucHk=) | `0.00% <0.00%> (ø)` | | | [src/criteria/auto\_pp2\_bp1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_pp2_bp1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fcHAyX2JwMS5weQ==) | `19.62% <0.00%> (+1.82%)` | :arrow_up: | | [src/criteria/auto\_pm1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_pm1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fcG0xLnB5) | `19.56% <7.14%> (-0.44%)` | :arrow_down: | | [src/criteria/auto\_pp3\_bp4.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_pp3_bp4.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fcHAzX2JwNC5weQ==) | `62.79% <10.00%> (-5.55%)` | :arrow_down: | | ... and [1 more](https://app.codecov.io/gh/bihealth/auto-acmg/pull/150?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth) | |