Adding gzip and VCF to the schema

[stschiff]

@nevrome I added the gzip-option to the README.md. How can I update the pdf? Can we perhaps add a little documentation for that? I think it's just some quarto command, right?

[TCLamnidis]

it's gzipping only allowed for geno and snp, but not ind?

i know fam files are not that large to need it, but "in for a penny in for a pound"?

[stschiff]

Yes, of course we can make this work as well. Right now, our implementation only supports gzip for those files that go through stream-processing, which is the SNP and Geno files and the VCF. I will create an issue on sequence-formats to allow zip there as well.

[nevrome]

About the .pdf building. I think you just have to render this quarto document: https://github.com/poseidon-framework/poseidon-schema/blob/master/toPDFviaQuarto.qmd

[stschiff]

OK, I just tried that, but unfortunately I cannot run quarto render here because of failing R dependencies (specifically package systemfonts is required and fails to install on both my Intel-iMac and my ARM64-Macbook).

[TCLamnidis]

I just pushed the rendered PDF

[stschiff]

Thanks. I've just made two minor changes, and I decided that I would like add also VCF support now to this Schema update. I have a PR to update trident for VCF writing support in the queue, so I think I will just keep this PR open until I've made that change, too. I will ping you, @TCLamnidis for re-generating the PDF again later.

[stschiff]

OK, I've added VCF. Could you please re-render the PDF, @TCLamnidis?

[TCLamnidis]

@stschiff Done!

[nevrome]

1. I wonder if we should add some more details about the respective file types. trident has this --inPlinkPopName flag, because .fam files can differ slightly. .bim files can have .s for the bases, which trident does not support (?). And for .vcf files trident only supports a certain subset of features, right? Maybe we should document/specify/enshrine some of these limitations here in the schema?

2. I suggest we don't render the .pdf version in these feature branches. We can do that when everything is collected in the dev branch 👍

[stschiff]

Yes, I guess indeed we could say a bit more about these formats. Not entirely trivial to document, though, as there are endless possibilities within these formats and I don't know in all cases what our limits are. I'll try to write something.