Impl. PathVertex::GetTaxaTree, enabled LCA testing & moved TaxaBreak forwards
scaffold_vertex.hpp & cpp:
- Made GetTaxaTree() member of PathVertex and EdgeIdVertex (both are
ScaffoldVertexes in the contracted DeBruijnGraph)
launcher.cpp:
- Added LCA parameter testing to start of repeat resolving step
read_cloud_connection_conditions.cpp & hpp:
- Made GetTaxaTree() part of the ScaffoldVertex itself (Edge- & Path-type)
scaffold_graph_construction_pipeline.cpp:
- Moved TaxaBreakConstructor to top of pipelines for efficiency
barcode_index_construction.cpp:
- Turned LCA settings tester back on
barcode_index_construction.cpp & hpp:
- Re-implemented taxonomy assignment with fuzzy_lca
- Some cleaner code in taxonomy assignment
- Added parameter testing module
- Bugfixes, header file updated
read_cloud_connection_conditions.cpp & hpp:
- Code cleanup (remove duplicated logic)
construction_callers & scaffold_graph_construction_pipeline:
- Nothing (just code that was commented out again)
Signed-off-by:
Overduin, Sam <sam.overduin@wur.nl>
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