bihealth / auto-acmg

Automatic classification of sequence variants and CNVs according to ACMG criteria.
GNU General Public License v3.0
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Implement pm2, ba1, bs1 rules #186

Closed gromdimon closed 2 months ago

gromdimon commented 2 months ago

Issue:

Description:

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 73.86935% with 156 lines in your changes missing coverage. Please review.

Project coverage is 84.78%. Comparing base (fba5e88) to head (60075e7). Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/criteria/auto_pm2_ba1_bs1_bs2.py 54.34% 21 Missing :warning:
src/vcep/coagulation_factor_deficiency.py 59.09% 18 Missing :warning:
src/vcep/brain_malformations.py 48.38% 16 Missing :warning:
src/vcep/enigma.py 46.66% 16 Missing :warning:
src/vcep/leber_congenital_amaurosis.py 50.00% 16 Missing :warning:
src/vcep/myeloid_malignancy.py 52.94% 16 Missing :warning:
src/vcep/rasopathy.py 50.00% 16 Missing :warning:
src/vcep/rett_angelman.py 46.66% 16 Missing :warning:
src/vcep/malignant_hyperthermia_susceptibility.py 55.17% 13 Missing :warning:
src/vcep/scid.py 94.73% 3 Missing :warning:
... and 3 more
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #186 +/- ## ========================================== - Coverage 86.43% 84.78% -1.66% ========================================== Files 63 63 Lines 3879 4437 +558 ========================================== + Hits 3353 3762 +409 - Misses 526 675 +149 ``` | [Files with missing lines](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?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/defs/auto\_acmg.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?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) | `99.59% <100.00%> (+<0.01%)` | :arrow_up: | | [src/vcep/acadvl.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Facadvl.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvYWNhZHZsLnB5) | `100.00% <100.00%> (ø)` | | | [src/vcep/cardiomyopathy.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Fcardiomyopathy.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvY2FyZGlvbXlvcGF0aHkucHk=) | `100.00% <100.00%> (ø)` | | | [src/vcep/cdh1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Fcdh1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvY2RoMS5weQ==) | `100.00% <100.00%> (ø)` | | | [src/vcep/congenital\_myopathies.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Fcongenital_myopathies.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvY29uZ2VuaXRhbF9teW9wYXRoaWVzLnB5) | `100.00% <100.00%> (ø)` | | | [src/vcep/dicer1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Fdicer1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvZGljZXIxLnB5) | `100.00% <100.00%> (ø)` | | | [src/vcep/epilepsy\_sodium\_channel.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Fepilepsy_sodium_channel.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvZXBpbGVwc3lfc29kaXVtX2NoYW5uZWwucHk=) | `100.00% <100.00%> (ø)` | | | [src/vcep/familial\_hypercholesterolemia.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Ffamilial_hypercholesterolemia.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvZmFtaWxpYWxfaHlwZXJjaG9sZXN0ZXJvbGVtaWEucHk=) | `100.00% <100.00%> (ø)` | | | [src/vcep/fbn1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Ffbn1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvZmJuMS5weQ==) | `100.00% <100.00%> (ø)` | | | [src/vcep/glaucoma.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree&filepath=src%2Fvcep%2Fglaucoma.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3ZjZXAvZ2xhdWNvbWEucHk=) | `100.00% <100.00%> (ø)` | | | ... and [26 more](https://app.codecov.io/gh/bihealth/auto-acmg/pull/186?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth) | |