Remove start_point concept from refine fit

bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

https://www.bacpop.org/poppunk

Apache License 2.0

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Remove start_point concept from refine fit #168

Closed johnlees closed 3 years ago

johnlees commented 3 years ago

This fixes some issues with manual start, and cleans up the code and makes it easier to follow. We no longer use a start point (haven't done for a while) which was a little useful with early pneumo models. Now we've optimised the global search instead.

nickjcroucher commented 3 years ago

Looks to be failing test python ../poppunk-runner.py --fit-model refine --ref-db example_db --output example_refine --neg-shift 0.8 --overwrite?

johnlees commented 3 years ago

Yeah sorry, fixing this locally. It's not quite doing the right thing yet either