Nicholas Knoblauch

In my use case I know that the file doesn't span multiple chromosomes, but yes, that's the idea. My (admittedly poor) understanding of the tabix format (for bcf/vcf files) is...

I think one could accomplish `bcftools merge A.bcf B.bcf -R

Thanks for the quick response! I appreciate that what you have now works for you and it's considerate of you to try to protect the user from making mistakes, but...

The error I get looks like this: ``` > gb gb$upload_file(src = "inst/foo.docx",dest = "Documents/foo.docx") Error in process_response(res, match.arg(http_status_handler), simplify) : Conflict (HTTP 409). Failed to complete operation. Message: A...

A mirror of the 1000 genomes ftp site is publicly available through [Azure Open Datasets](https://learn.microsoft.com/en-us/azure/open-datasets/dataset-1000-genomes)

I don't know if you'd consider this a hack or not, but couldn't you run the lmod init script using [shell.prefix?](https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-want-to-configure-the-behavior-of-my-shell-for-all-rules-how-can-that-be-achieved-with-snakemake)

I'm not sure what this means: > the module commands are prepended even to shell.prefix Could you give a little more information as to what it is you're doing specifically...

I'm not too familiar with plink/plink2 internals but it was my understanding that sample size is computed from the fam file (or equivalent), and the number of variants is computed...

That's likely because `xxHash` is installed somewhere outside what's pointed to by `LD_LIBRARY_PATH`. One way around that would be to vendor `xxHash`(e.g include it as a submodule). Might as well...

Has there been any progress on this? I'd be happy to make a pull request.