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sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
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Variant positions less than one? #1176

Open hyanwong opened 10 months ago

hyanwong commented 10 months ago

I'm assuming that variant positions must be 1 or greater in an sgkit dataset. Is this part of the spec, or enforced anywhere? I looked through the docs and couldn't find anything. I assume setting position to -1 will also break stuff?

In tskit the positions start at 0, so there's a bit of trickery needed in my use-case, I suspect.

tomwhite commented 9 months ago

Variant positions can start at 0 or 1 - it's not enforced in sgkit. There's some discussion in #434.

I assume setting position to -1 will also break stuff?

I'm not sure. What's the use case?