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Improved taxonomy assignment & implemented taxonomy transition filter.
barcode_index.hpp: - Initialized TaxIdEncoder with "0" taxatree - Added func TaxIdEncoder::ToTaxaTreeVector - Bugfix EdgeEntry::GetTaxonomy() barcode_info_extractor.hpp: - Added funcs: ToTaxaTreeVector, TaxaTreeFromTaxId, GetTaxaTreeFromEdge barcode_index_construction.cpp: - Moved ToTaxaTreeVector to extractor & barcode_index - Improved majority_vote_lca to actually use LCA construction_callers.cpp & hpp: - Added TaxaBreakConstructorCaller to break mismatched taxa in contracted assembly graph read_cloud_connection_conditions.cpp: - Added TaxaBreakPredicate that returns false when transition (scaffold_edge) has incompatible taxonomy scaffold_graph_construction_pipeline.cpp: - Added TaxaBreak routine to basic mode & scaffolding mode
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- src/common/barcode_index/barcode_index.hpp 17 additions, 2 deletionssrc/common/barcode_index/barcode_index.hpp
- src/common/barcode_index/barcode_info_extractor.hpp 16 additions, 0 deletionssrc/common/barcode_index/barcode_info_extractor.hpp
- src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/construction_callers.cpp 24 additions, 0 deletions...tend/scaffold_graph_construction/construction_callers.cpp
- src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/construction_callers.hpp 23 additions, 0 deletions...tend/scaffold_graph_construction/construction_callers.hpp
- src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/read_cloud_connection_conditions.cpp 38 additions, 0 deletions...d_graph_construction/read_cloud_connection_conditions.cpp
- src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/read_cloud_connection_conditions.hpp 16 additions, 0 deletions...d_graph_construction/read_cloud_connection_conditions.hpp
- src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp 5 additions, 0 deletions...aph_construction/scaffold_graph_construction_pipeline.cpp
- src/projects/spades/barcode_index_construction.cpp 52 additions, 33 deletionssrc/projects/spades/barcode_index_construction.cpp
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