ivargr

I've added a small tool in kage now that lets you convert the vcf so that genotypes are diploid before running KAGE. I think that might be an okay solution...

I see! I think I maybe understand the VCF now. So I assume for instance BG_hap1_chr01 and BG_hap2_chr01 are the two haplotypes from the same individual? If that is the...

It seems the problem now is that some of your variants contains Ns, which is not ideal as KAGE is not able to compute kmers for them. Unfortunately, the error...

The fix now is not ignoring variants with Ns completely, but instead is just encoding Ns as A instead as a "hack" to be able to compute kmers. From my...

Hi! It seems the system is running out of memory: `numpy.core._exceptions._ArrayMemoryError: Unable to allocate 204. GiB for an array with shape (27376795028,) and data type int64` Can I ask how...

I've looked into this now, and think there might ba possible problem with increased memories in some part of the indexing process if some variant alleles are very big. I've...

Great! Let me know if you run into any other issues while genotypig :)

Hi! Thanks for reaching out. I think Python 3.8 should work fine. Would you be able to just copy-paste the whole log from the installation process, and then I can...

Hi! I looked into this and I think the problem is the Python version, as some of the packages KAGE depends on does not support Python 3.12. Could you try...

Sorry, I was a bit quick to assume 3.12 was the issue. Seems the problem is compiling the C code in one of KAGE's dependencies, SharedArray. Could you try doing...