Overduin, Sam authored Feb 06, 2020 and Overduin, Sam committed Feb 06, 2020

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>