1. 03 Dec, 2019 1 commit
    • Overduin, Sam's avatar
      Improved taxonomy assignment & implemented taxonomy transition filter. · 5b1631c0
      Overduin, Sam authored and Overduin, Sam's avatar Overduin, Sam committed
      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
      5b1631c0
  2. 29 Nov, 2019 1 commit
    • Overduin, Sam's avatar
      barcode_index_builder.hpp: · ba6cfe86
      Overduin, Sam authored and Overduin, Sam's avatar Overduin, Sam committed
      - Added no TaxaTree in read means taxa '0'
      - Bugfix taxatree_prefixes
      - Cut out taxatree parser to vector<int>
      
      barcode_index.hpp:
      - Changed TaxIdEncoder to fully use TaxId vs int64
      - small bugfixes eg: moved declarations around, corrected taxid_begin()
      - made edge_to_entry in FrameBarcodeIndex public
      
      barcode_info_extractor.hpp:
      - Added GetTaxidCount
      
      barcode_index_construction.cpp:
      - Added chunk of code to determine and set LCA per EdgeEntry in barcode_index
      ba6cfe86
  3. 27 Nov, 2019 1 commit
    • Overduin, Sam's avatar
      barcode_index_builder.hpp: · d471de51
      Overduin, Sam authored and Overduin, Sam's avatar Overduin, Sam committed
      - Added TaxaTree (like 1.23.456.7890) parser from reads & store in index
      
      barcode_index.hpp:
      - Added data structure in BarcodeIndex to store TaxaTree mapping
        to taxids (taxatree_codes_).
      - Added data structure in EdgeEntry to store taxid_distribution_.
      - Added attribute to EdgeEntry for taxonomy_.
      
      barcode_info_extractor.hpp:
      - Added method to get taxids for a EdgeID
      d471de51
  4. 22 Nov, 2019 1 commit
  5. 18 Nov, 2019 1 commit