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config.info: - Added taxonomy false. barcode_index_builder.hpp: - only extract TaxaTree if cfg::get().taxonomy scaffold_graph_construction_pipeline.cpp: - only add TaxaBreak constructor if cfg::get().taxonomy config_struct.cpp & hpp: - added taxonomy to cfg. barcode_index_construction.cpp: - Only decide LCA if cfg::get().taxonomy spades_iteration_stage.py: - Add taxonomy option to config.info of final iteration options_parser.py: - Add --taxonomy argument. Only usable with --meta and --gemcode options. Some various other clean-ups in files: - aa_todo_notes - path_polisher.hpp - path_scaffolder.cpp - scaffold_vertex.cpp Signed-off-by: Overduin, Sam <sam.overduin@wur.nl>
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