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Pedigree topological order

See original GitHub issue

Many pedigree algorithms require the topological ordering of nodes such that each individual occurs before its decedents. In sgkit it makes sense to simply calculate and store the topological order as an array of indices. This array can be calculated from the parent array introduced in #839. There are several graph libraries which could be used to compute topological order https://github.com/pystatgen/sgkit/discussions/786#discussioncomment-1863520. Alternatively we could implement Kahn’s algorithm to avoid picking up another dependency (it’s quite simple).

Either way the API is quite simple e.g. topological_sort(ds, parent=parent) -> ds with topological_order where topological_order has dimension samples and is of type uint64. Suggestions for better names are welcome!

Issue Analytics

State:
Created a year ago
Comments:6

Top GitHub Comments

1reaction

jeromekellehercommented, Apr 22, 2022

Great idea @timothymillar. I suspect it would be simpler to just implement this ourselves. We have an implementation in tskit we can compare against:

0reactions

timothymillarcommented, May 1, 2022

Done in #846

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