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(1) Should be fine - I've used it a fair bit with 4.0.0 beta 2 with no problems
(2) Yes, use nucmer.Runner(reference_file, query_file, results_file, promer=True)
To be honest, what little documentation there is is awful (the repo was really made for me to use in other projects). If it's getting used by people other than me and this comment gets enough thumbs up, then I'll write some proper docs for it.
@martinghunt Could you please clarify two points:
(1) Does pymummer support mummer4?
(2) Does it support promer in addition to nucmer?
Thanks!
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