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KangchengHou / admix-kit

Toolkit for analyzing genetics data from admixed populations
https://kangchenghou.github.io/admix-kit
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Feature request: provide separate input paths for pgen, psam, pvar, lanc #30

Closed michaelofrancis closed 3 months ago

michaelofrancis commented 3 months ago

Hi,

Right now user is only able to load in pfile and lanc when they all have the same stem and are in the same directory. This is inconvenient and it would be really great to be able to load in separate file paths for each if desired. This applies to most/all of the existing functions.

Thanks, Mike

KangchengHou commented 3 months ago

.lanc files always being coupled with .pgen / .psam / .pvar files is designed in the same spirit that PLINK2 files always come in triples. It would require many changes to the command line interface to incorporate the feature that .lanc can be loaded seperately - currently sorry that I do not have enough bandwidth to incorporate this. As a quick fix, I suggest to have soft link ln -s to link .lanc files from other directories.

michaelofrancis commented 3 months ago

Hi, I imagine most researchers will have dedicated directories for pfiles that they will not want to add .lanc files to. I suppose I could create a directory which has symlinks for all four of the files and this would be fine. Thank you.