tsinfer
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Low density regions and splitting
Currently for large scale inference were splitting at regions of low, or no, site density. This results in some chrom arms with 3-4 tree sequences, which is annoying for downstream analysis. To over come this we either
- Rejoin after inference
- Tell tsinfer to terminate ancestor generation at the boundaries of drop out regions, this would mean that no edges span the bad regions.
It feels like option 2 is correct here and wouldn't be too tough to implement. Interested in others thoughts here. @jeromekelleher, @hyanwong