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scaffold_vertex.hpp & cpp: - Used Fuzzy LCA for PathVertex::GetTaxaTree with max_drilldown_ratio=0.4, max_mismatch_ratio=0.03 and min_assignment_ratio=0.3. This code is in barcode_index_construction.cpp barcode_index.hpp & barcode_index_builder.hpp: - added code to deal with "_SUBSTR(0,106)" at end of read names (influenced taxatrees). launcher.cpp: - Removed LCA parameter testing to start of repeat resolving step read_cloud_connection_conditions.cpp & hpp: - Output which edge connections (or path connections) are being broken in logfile. scaffold_graph_construction_pipeline.cpp: - Moved TaxaBreakConstructor to bottom of pipelines for more informative breaks. path_scaffolder.cpp: - map.at() replaced with map[] if item not within map. Added debuggin msg. barcode_index_construction.cpp: - Added function to get LCA for PathScaffoldVertex (more conservative than reads-> contig LCA). - Started prototype code for taxonomy assignment per edges (eg. using CAT) Signed-off-by: Overduin, Sam <sam.overduin@wur.nl>
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