- 12 Mar, 2020 5 commits
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Overduin, Sam authored
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Overduin, Sam authored
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Overduin, Sam authored
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Overduin, Sam authored
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Overduin, Sam authored
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- 05 Mar, 2020 1 commit
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Overduin, Sam authored
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- 28 Feb, 2020 1 commit
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Overduin, Sam authored
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- 25 Feb, 2020 1 commit
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Overduin, Sam authored
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- 24 Feb, 2020 4 commits
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Signed-off-by:
Overduin, Sam <sam.overduin@wur.nl>
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Overduin, Sam authored
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Overduin, Sam authored
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Overduin, Sam authored
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- 21 Feb, 2020 2 commits
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Overduin, Sam authored
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config.info: - Added taxonomy false. barcode_index_builder.hpp: - only extract TaxaTree if cfg::get().taxonomy scaffold_graph_construction_pipeline.cpp: - only add TaxaBreak constructor if cfg::get().taxonomy config_struct.cpp & hpp: - added taxonomy to cfg. barcode_index_construction.cpp: - Only decide LCA if cfg::get().taxonomy spades_iteration_stage.py: - Add taxonomy option to config.info of final iteration options_parser.py: - Add --taxonomy argument. Only usable with --meta and --gemcode options. Some various other clean-ups in files: - aa_todo_notes - path_polisher.hpp - path_scaffolder.cpp - scaffold_vertex.cpp Signed-off-by:
Overduin, Sam <sam.overduin@wur.nl>
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- 06 Feb, 2020 1 commit
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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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- 15 Jan, 2020 1 commit
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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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- 08 Jan, 2020 1 commit
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barcode_index.hpp: - Improved robustness of some functions (error handling) - Added taxid_distribution serialisation 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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- 06 Dec, 2019 1 commit
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barcode_index.hpp: - Implemented taxa_codes + taxonomy_ serialisation - Made taxa_codes::map's public barcode_info_extractor.hpp: - Added funcs: EdgeIsValid, GetConjugateEdge, GetSequence, GetEdgeLength barcode_index_construction.cpp: - Added write_contigs_to_fasta for testing purposes. - Re-implemented taxonomy assignment to use edge & conjugate. read_cloud_connection_conditions.cpp: - In TaxaBreakPred.: if taxonomy of edge not found, try taxonomy of conjugate edge. Else taxa 0. logger.hpp: - Created special DEBUG_SAM for personal logging. Will change at end.
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- 03 Dec, 2019 1 commit
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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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- 29 Nov, 2019 1 commit
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- 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
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- 27 Nov, 2019 1 commit
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- 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
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- 22 Nov, 2019 1 commit
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Overduin, Sam authored
Changed scope of static const MAGIC_LOOP_CONSTANT due to CLion build process complaining. Shouldn't break anything. Also uploaded aa_todo_notes. In future will not mention this file.
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- 18 Nov, 2019 1 commit
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Overduin, Sam authored
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