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brentp / somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
MIT License
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meaning of warning:cant use more than 65535 sites #48

Open danrlu opened 4 years ago

danrlu commented 4 years ago

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!

brentp commented 4 years ago

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.

danrlu commented 4 years ago

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

brentp commented 4 years ago

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.

danrlu commented 4 years ago

Got it. Thank you!