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meaning of warning:cant use more than 65535 sites

Open danrlu opened this issue 4 years ago • 4 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!

danrlu avatar Apr 16 '20 21:04 danrlu

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.

brentp avatar Apr 16 '20 22:04 brentp

Good to know! If the sites file has more sites, do the first 65535 sites get used?

danrlu avatar Apr 17 '20 02:04 danrlu

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.

brentp avatar Apr 17 '20 14:04 brentp

Got it. Thank you!

danrlu avatar Apr 18 '20 00:04 danrlu