[GEN-1067] add functionality to warn for identical ref and tsa2

Sage-Bionetworks / Genie

Validation and processing of GENIE files

https://genie.synapse.org/

MIT License

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[GEN-1067] add functionality to warn for identical ref and tsa2 #553

Closed danlu1 closed 6 months ago

danlu1 commented 7 months ago

Purpose: This PR includes changes in _check_tsa1_tsa2 function of maf.py to throw errors (column level and row level) when REFERENCE_ALLELE is equal to TUMOR_SEQ_ALLELE2.

Test:

Unit tests are included.
Updated GOLD center file and Test center file and ran validation locally and on ec2 instance.

rxu17 commented 7 months ago

Also don't forget to make sure your build is successful, i think there's just some formatting to adjust in your code: https://github.com/Sage-Bionetworks/Genie/actions/runs/8237606927/job/22526728071?pr=553

If you have black installed, you can just run black on everything using black . (which will auto-lint your code) then commit and push the formatting changes.

sonarcloud[bot] commented 6 months ago

Quality Gate passed

Issues
5 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud