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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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Reimplement AutoPS1PM5 #130

Closed gromdimon closed 2 months ago

gromdimon commented 2 months ago

Issue:

Description: N/A

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 40.90909% with 39 lines in your changes missing coverage. Please review.

Project coverage is 63.00%. Comparing base (0906b77) to head (8d74f35).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #130 +/- ## ========================================== + Coverage 60.29% 63.00% +2.71% ========================================== Files 28 28 Lines 2637 2633 -4 ========================================== + Hits 1590 1659 +69 + Misses 1047 974 -73 ``` | [Files](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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/api/annonars.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?src=pr&el=tree&filepath=src%2Fapi%2Fannonars.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2FwaS9hbm5vbmFycy5weQ==) | `85.36% <100.00%> (+0.36%)` | :arrow_up: | | [src/auto\_acmg.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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==) | `84.44% <100.00%> (ø)` | | | [src/criteria/auto\_bp7.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_bp7.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fYnA3LnB5) | `32.29% <100.00%> (+11.67%)` | :arrow_up: | | [src/criteria/auto\_pp3\_bp4.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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==) | `66.66% <100.00%> (+50.96%)` | :arrow_up: | | [src/defs/annonars\_variant.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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% <ø> (ø)` | | | [src/pvs1/auto\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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) | `79.41% <100.00%> (-0.59%)` | :arrow_down: | | [src/pvs1/seqvar\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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=) | `51.11% <100.00%> (ø)` | | | [src/pvs1/strucvar\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?src=pr&el=tree&filepath=src%2Fpvs1%2Fstrucvar_pvs1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL3B2czEvc3RydWN2YXJfcHZzMS5weQ==) | `33.00% <0.00%> (ø)` | | | [src/criteria/auto\_ba1\_bs1\_bs2\_pm2.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?src=pr&el=tree&filepath=src%2Fcriteria%2Fauto_ba1_bs1_bs2_pm2.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2NyaXRlcmlhL2F1dG9fYmExX2JzMV9iczJfcG0yLnB5) | `23.52% <0.00%> (+0.27%)` | :arrow_up: | | [src/criteria/auto\_pm1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?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) | `21.05% <0.00%> (+0.27%)` | :arrow_up: | | ... and [4 more](https://app.codecov.io/gh/bihealth/auto-acmg/pull/130?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth) | |