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Merge back large change to add_gfa_build_pangenome

Workum, Dirk-Jan van requested to merge rewrite_legacy_code_node_localization_for_gfa_build_pangenome into add_gfa_build_pangenome

Created a separate branch for this possibly breaking change of build_pangenome. I changed the localization process written by Mathijs to be able to deal with any overlap between nodes; not yet properly tested. This enables any GFA to be loaded as graph layout instead of only cDBG (since cDBG assumes K - 1 overlap between all nodes).

Apart from the end-to-end pipeline here at git.wur.nl running successfully, testing the following before merging:

  • Covid MC GFA
  • Covid PGGB GFA
  • Covid PanTools GFA
  • Arabidopsis MC GFA
  • Arabidopsis PGGB GFA
  • Arabidopsis PanTools GFA
Edited by Workum, Dirk-Jan van

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