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I think this is all OK. As long as the compiler is happy, I'm as well. I opened #39 to address what you mentioned above. I don't think the snpSet is important here, but vcf writing could be useful. Would it be OK to just go diploid by default? |
Additional adjustments in the generator modules
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nevrome
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Mar 16, 2026
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This is a first attempt to update the code-base to poseidon-hs-1.6.9.1 and stackage lts-22.43.
@nevrome needs to definitely review and maybe also extend AdmixPops. Right now I do not support VCF writing, which would be very easy to implement, but I failed to do it because the current
writeVCFAPI from poseidon-hs requires a Janno file (so that the VCF writing can write out group names and sex). Perhaps we should change the writeVCF API to make this simpler and not dependent on Janno. Another thing is that I currently do not output a SNpSET with AdmixPops. This could be changed, since the input SNP sets are known. But I did not have time to look into the exact machinery of AdmixPops to understand what the input packages exactly are. Maybe you could implement that, @nevrome, based on the Forge codebase, which has all the Snippets necessary here. Same is true for writeVCF.