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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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Cycles in graph #134

Closed egoltsman closed 3 years ago

egoltsman commented 3 years ago

Hello, The first paragraph in the README mentions that the goal is a locally acyclic graph. I recall seqwish not having this requirement, i.e. it used to happily built cyclic graphs. Did the graph model change in seqwish or is it just being called with some constraints on cycles?

This ticket suggests it might be the latter, but could you confirm? https://github.com/ekg/seqwish/issues/19

Thank you for continuing your work in this direction!

AndreaGuarracino commented 3 years ago

Hi @egoltsman, you recall right that seqwish has no such requirement. The 'local acyclicity' is introduced during the smoothing phase with smoothxg, which locally applies Partial Order Alignments that result in acyclic graphs.