Commits · optimized-map · bioinformatics / PanTools · GitLab

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May 10, 2022
- Tiny documentation fix. · 72bbc6ac
  Moed, Matthijs authored 3 years ago
  
  72bbc6ac
- Cache property keys when mapping. · c25f2a6b
  Moed, Matthijs authored 3 years ago
  
  c25f2a6b
Apr 20, 2022
- Add offsets cache to explore_node(). · 5e06d875
  Moed, Matthijs authored 3 years ago
  
  5e06d875
- Redundant comment. · 117961c1
  Moed, Matthijs authored 3 years ago
  
  117961c1
- More refactoring on explore_node(). · 42bb0c7b
  Moed, Matthijs authored 3 years ago
  
  42bb0c7b
- Move pangenomic address extraction in explore_node() to separate class. · a960b920
  Moed, Matthijs authored 3 years ago
  
  a960b920
- Small textual changes. · e8d5e7bd
  Moed, Matthijs authored 3 years ago
  
  e8d5e7bd
- Refactor cryptic formula in explore_node() to separate method. · 06e94205
  Moed, Matthijs authored 3 years ago
  
  06e94205
- Small readability improvements to explore_node(). · cbb5d033
  Moed, Matthijs authored 3 years ago
  
  cbb5d033
- Move variables in GenomeLayer::Map::explore_node() to appropriate scope. · f537ab5c
  Moed, Matthijs authored 3 years ago
  
  f537ab5c
- Move retrieving node length property in mapping to appropriate scope. · f06064e9
  Moed, Matthijs authored 3 years ago
  
  f06064e9
Apr 07, 2022
- Implemented a few caches to improve mapping performance. · c29f75ab
  Moed, Matthijs authored 3 years ago
  
  c29f75ab
Apr 06, 2022
- Merge branch 'uniquify_msa_headers' into 'master' · 1afdc26d
  Workum, Dirk-Jan van authored 3 years ago
  1afdc26d
- removing identifiers_incorrect_for_fasttree and uniquifying all sequences that are input for MSA · 9cdfa626
  Workum, Dirk-Jan van authored 3 years ago
  
  9cdfa626
Mar 29, 2022
- Merge branch 'consensus_tree_no_polytomies' into 'master' · ac129698
  Workum, Dirk-Jan van authored 3 years ago
  ac129698
- make ignoring of polytomies default for ASTRAL-PRO · c77d2a06
  Workum, Dirk-Jan van authored 3 years ago
  
  c77d2a06
Mar 25, 2022
- Merge branch 'high_freq_kmer_classification' into 'master' · 9d318ee3
  Jonkheer, Eef authored 3 years ago
  9d318ee3
Mar 21, 2022
- Resolved an issue where generated to many warnings · 460be8f3
  Eef Jonkheer authored 3 years ago
  
  460be8f3
- Merge branch 'master' into high_freq_kmer_classification · a7216a0c
  Eef Jonkheer authored 3 years ago
  
  a7216a0c
Mar 18, 2022
- Merge branch 'hotfix_core_snp_tree' into 'master' · f2d9e35a
  Workum, Dirk-Jan van authored 3 years ago
  f2d9e35a
Mar 17, 2022
- let core_snp_tree and consensus_tree print progress · 9cfb6eec
  Workum, Dirk-Jan van authored 3 years ago
  
  9cfb6eec
Mar 14, 2022
- let core_snp_tree search for alignment with updated msaNames variable instead... · a0b7bf0e
  Workum, Dirk-Jan van authored 3 years ago
  a0b7bf0e
Mar 09, 2022
- Merge branch 'add_fasttree_options_to_msa' into 'master' · 15c9d876
  Workum, Dirk-Jan van authored 3 years ago
  15c9d876
- small improvement to running fasttree · 76efefe7
  Workum, Dirk-Jan van authored 3 years ago
  
  76efefe7
Feb 25, 2022
- Merge branch 'remove-netbeans' into 'master' · d4dfc6ba
  Jonkheer, Eef authored 3 years ago
  d4dfc6ba
Feb 24, 2022
- Delete NetBeans-specific files and directories. Close #9 . · ac8ca616
  Moed, Matthijs authored 3 years ago
  
  ac8ca616
Feb 22, 2022
- outlining message in add_phenotype · 1353d1a2
  Eef Jonkheer authored 3 years ago
  
  1353d1a2
- Stop when to many sequences in · b3c82eed
  Eef Jonkheer authored 3 years ago
  
  b3c82eed
- Merge branch 'metrics_bugfix' into 'master' · 8baa942c
  Jonkheer, Eef authored 3 years ago
  8baa942c
- removed typo · 597e8951
  Eef Jonkheer authored 3 years ago
  
  597e8951
Feb 21, 2022
- Rollback annotation when annotation unsuccessful · 3db9a83a
  Eef Jonkheer authored 3 years ago
  
  3db9a83a
- Merge branch 'antismash_update' into 'master' · 338de3f7
  Jonkheer, Eef authored 3 years ago
  338de3f7
- Corrected some typos and spelling mistakes · 141c83f5
  Eef Jonkheer authored 3 years ago
  
  141c83f5
Feb 18, 2022
- Added to general --help · a59b9c77
  Eef Jonkheer authored 3 years ago
  
  a59b9c77
- Print error message when no gene identifiers in antismash input · 331b865d
  Eef Jonkheer authored 3 years ago
  
  331b865d
- Merge branch 'master' into antismash_update · 6ce1da10
  Eef Jonkheer authored 3 years ago
  
  6ce1da10
- Merge branch 'hotfix_msa_protein_alignment_trees' into 'master' · 118de4b7
  Workum, Dirk-Jan van authored 3 years ago
  118de4b7
- Hotfix msa protein alignment trees · 3ab1f29e
  Workum, Dirk-Jan van authored 3 years ago
  
  3ab1f29e
- Merge branch 'include_version' into 'master' · 03006e21
  Workum, Dirk-Jan van authored 3 years ago
  03006e21
- Include version and commit ID · 91c0f301
  Workum, Dirk-Jan van authored 3 years ago
  
  91c0f301