meaning of warning:cant use more than 65535 sites
danrlu opened this issue · comments
When running somalier extract I got a warning message:
warning:cant use more than 65535 sites
What does this mean? Should we reduce the number of variants we feed into somalier?
I'm using version: 0.2.9
Thanks for writing this great tool!
somalier currently only supports 65535 sites. did you make a custom sites file with more than that?
you can use the sites files distributed with somalier or make sure yours has fewer than that amount.
if there's broad need, I could relax that constraint, but for estimating relatedness, that is more than enough.
Good to know! If the sites file has more sites, do the first 65535 sites get used?
hmm. actually it gives a warning, but doesn't do anything about it. I will fix that for next release (and truncate to that number), but you should not use the .somalier files that were created with a sites file with more sites as it will likely result in undefined behavior.
Got it. Thank you!