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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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Refactor codebase for better internal data structure #159

Closed gromdimon closed 1 month ago

gromdimon commented 1 month ago

N/A

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 38.83041% with 523 lines in your changes missing coverage. Please review.

Project coverage is 44.66%. Comparing base (7be0841) to head (9c5de27).

Files Patch % Lines
src/auto_acmg.py 23.07% 80 Missing :warning:
src/criteria/auto_pm2_ba1_bs1_bs2.py 18.68% 74 Missing :warning:
src/criteria/auto_pvs1.py 14.45% 71 Missing :warning:
src/criteria/auto_pp3_bp4.py 20.68% 69 Missing :warning:
src/criteria/auto_pm4_bp3.py 22.22% 49 Missing :warning:
src/criteria/auto_pp2_bp1.py 15.51% 49 Missing :warning:
src/criteria/auto_pm1.py 19.60% 41 Missing :warning:
src/criteria/auto_ps1_pm5.py 26.53% 36 Missing :warning:
src/criteria/auto_bp7.py 30.23% 30 Missing :warning:
src/defs/auto_acmg.py 96.44% 6 Missing :warning:
... and 6 more
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #159 +/- ## ========================================== - Coverage 50.20% 44.66% -5.54% ========================================== Files 35 33 -2 Lines 3420 3132 -288 ========================================== - Hits 1717 1399 -318 - Misses 1703 1733 +30 ``` | [Files](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?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/annonars\_gene.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree&filepath=src%2Fdefs%2Fannonars_gene.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvYW5ub25hcnNfZ2VuZS5weQ==) | `100.00% <100.00%> (ø)` | | | [src/defs/annonars\_range.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?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/159?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\_pvs1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree&filepath=src%2Fdefs%2Fauto_pvs1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvYXV0b19wdnMxLnB5) | `100.00% <100.00%> (+1.12%)` | :arrow_up: | | [src/defs/genome\_builds.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree&filepath=src%2Fdefs%2Fgenome_builds.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2RlZnMvZ2Vub21lX2J1aWxkcy5weQ==) | `100.00% <100.00%> (ø)` | | | [src/defs/seqvar.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?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) | `90.62% <100.00%> (-2.16%)` | :arrow_down: | | [src/defs/strucvar.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?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=) | `90.76% <100.00%> (ø)` | | | [src/bench/comparison\_v0.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree&filepath=src%2Fbench%2Fcomparison_v0.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2JlbmNoL2NvbXBhcmlzb25fdjAucHk=) | `0.00% <0.00%> (ø)` | | | [src/bench/comparison\_v1.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree&filepath=src%2Fbench%2Fcomparison_v1.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2JlbmNoL2NvbXBhcmlzb25fdjEucHk=) | `0.00% <0.00%> (ø)` | | | [src/bench/comparison\_v2.py](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree&filepath=src%2Fbench%2Fcomparison_v2.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth#diff-c3JjL2JlbmNoL2NvbXBhcmlzb25fdjIucHk=) | `0.00% <0.00%> (ø)` | | | ... and [13 more](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth) | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/bihealth/auto-acmg/pull/159/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bihealth)