Chiara Rasi

Replace alchy with sqlservice and unfreeze SQLAlchemy

1

### This PR adds | fixes: - Fix #251 **How to prepare for test**: - Install in a local conda env -> pip install -e . (I've tested it with...

Replace deprecated Alchy with SQLAlchemy

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Alchy is discontinued and integrating chanjo in other software prevents software upgrades, see - https://github.com/Clinical-Genomics/scout/issues/4614 - https://github.com/Clinical-Genomics/scout/issues/4101

pymysql.err.OperationalError: `(1055, "Expression #1 of SELECT list is not in GROUP BY clause and contains nonaggregated column 'chanjo4.transcript_stat.id' which is not functionally dependent on columns in GROUP BY clause; this...

Customer request to modify the --distance param in VEP from 5Kb to 500Kb

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I'm dropping here a user question/request from the customer support ticket ([#372436](https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=51204)): Pertaining to the issue of SVs and specifically BND, we are trying to look for the following recurrent...

Hello, I noticed that this bug is still not fixed. Here comes a suggestion for a fix! (fix #45 ) ### Current master branch: ``` (base) chiararasi@n181-p119 d4-format % docker...

We should stop supporting python 3.8, see https://pythonspeed.com/articles/stop-using-python-3.8/

Hello! It's not a huge deal but today It took us a while to understand why the stats returned always 0 for one of our samples. Basically if the sample...