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jeromekelleher / sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Classify non tree hmms #123

Closed hyanwong closed 1 year ago

hyanwong commented 1 year ago

Add an extra column to say if the HMM-reported breakpoint does not make it into the final ARG

hyanwong commented 1 year ago

It would be good to merge this @jeromekelleher, as I can then use it for the paper plots. Nothing controversial here now.

jeromekelleher commented 1 year ago

Needs rebasing I think. I see we're still using the causal sample map (which I'm sure is wrong), I'll go through and make some changes once this is in.

hyanwong commented 1 year ago

OK - I didn't realise it was plain wrong, sorry! Definitely worth correcting. Now rebased.

hyanwong commented 1 year ago

Thanks if you can see to the causal sample map thing. You'd be quicker at it than I would.