Jonas Freimuth

Ok great, after some time I also got this one on main, I will reopen #18: ``` =================================================================================== test session starts ==================================================================================== platform linux -- Python 3.10.12, pytest-7.4.2, pluggy-1.3.0 rootdir:...

Hello, here is a little update: I am currently working on enabling direct `vcf` input. However, there are some INFO fields that need to be present, namely Allele Frequency (`AF`)...

FYI, development of that branch will now take place on [predef-rule-io-dev](https://github.com/jonasfreimuth/pigx_sars-cov-2/tree/predef-file-io-dev), due to git reasons

The changes are now merged into main in #142. But I have no updates on getting nucleotide info from the files @sinclairify provided.

Could you please clarify which data are downloaded from covidCG (e.g. the query) and the format the downloaded tables have?

Also this is the same issue as in #68.

[This commit](https://github.com/BIMSBbioinfo/pigx_sars-cov-2/commit/8f941534be1a96c8e329a02858f826221db09d82) already makes a lot of things in the variantreport dynamic. But lofreq params are still not adjustable. Also I don't understand what parameters you mean in the QC...

I would consider this resolved once we are able to get distcheck working, which will should be possible with the changes on [here](https://github.com/jonasfreimuth/pigx_sars-cov-2/tree/get-build-to-work) (which boil down to having extra rules...

For the moment it is not computed from read lengths, but possible to set it from the settings file...

Also I don't see how iVar allows setting percentages for read-length. Either we would have to process every read individually (involving a lot of overhead, I can't see how this...