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Merge branch develop into phased_pangenomics

Merging develop into phased_pangenomics. This caused some issues, which are being fixed in this branch.

TODO in this merge request:

  • Fix gene_classification
  • Fix ANI
  • Fix core_snp_tree
  • Make sure all variant code works
  • Clean up
Edited by Workum, Dirk-Jan van

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