Commits · cb221b72b428fe2e21ab7ce4f8b3c9dcfcafeb9e · bioinformatics / PanTools · GitLab

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May 16, 2025
- Fixed merge conflicts · cb221b72
  Flege, Patrick authored 2 months ago
  
  cb221b72
May 15, 2025
- Merge branch 'ensure_busco_exists_before_optimal_grouping' into 'develop' · fb4a46f0
  Workum, Dirk-Jan van authored 2 months ago
  fb4a46f0
- Changed documentation (CHANGELOG and rst-file) and fixed previous error in MessageBundle · 1e3e5f32
  Flege, Patrick authored 2 months ago
  
  1e3e5f32
May 14, 2025
- Changed documentation to account for different kinds of sequence elements · f5434c07
  Flege, Patrick authored 3 months ago
  
  f5434c07
- Updated test · b663e7f9
  Flege, Patrick authored 3 months ago
  
  b663e7f9
- Modified according to review comments · 5e162ce0
  Flege, Patrick authored 3 months ago
  
  5e162ce0
- Updated logging from debug to trace · c842ea49
  Flege, Patrick authored 3 months ago
  
  c842ea49
May 12, 2025
- update changelog · f4639056
  Workum, Dirk-Jan van authored 3 months ago
  
  f4639056
- make sure skip arrays are initialised · 33dac62d
  Workum, Dirk-Jan van authored 3 months ago
  
  33dac62d
- check that BUSCO has been run before starting optimal_grouping logic · 05653505
  Workum, Dirk-Jan van authored 3 months ago
  
  05653505
- Updated according to review comments · c65ca868
  Flege, Patrick authored 3 months ago
  
  c65ca868
Apr 30, 2025
- Merge branch 'remove_useless_proteome_tests' into 'develop' · 4e5c1874
  Workum, Dirk-Jan van authored 3 months ago
  4e5c1874
Apr 29, 2025
- remove useless proteomelayertest which only caused confusion · 8320900a
  Workum, Dirk-Jan van authored 3 months ago
  
  8320900a
Apr 28, 2025
- deleted local test files · 8be85e89
  Flege, Patrick authored 3 months ago
  
  8be85e89
- Insert docstrings · 34512106
  Flege, Patrick authored 3 months ago
  
  34512106
- Refactoring · eb2a8bd2
  Flege, Patrick authored 3 months ago
  
  eb2a8bd2
- Merge branch 'develop' into feature/fix-msa-with-threshold · 7116c6f2
  Flege, Patrick authored 3 months ago
  
  7116c6f2
Apr 25, 2025
- Refacotring · 43bfd553
  Flege, Patrick authored 3 months ago
  
  43bfd553
Apr 24, 2025
- Refactoring and logging to replace MSA flow with equicalent logic in gapcalculator · 818987bb
  Flege, Patrick authored 3 months ago
  
  818987bb
Apr 23, 2025
- Merge branch 'update_documentation_phenotypes' into 'develop' · b940473a
  Workum, Dirk-Jan van authored 3 months ago
  b940473a
- Merge branch 'update_reference_commit_vcf_change' into 'develop' · bcb1166b
  Workum, Dirk-Jan van authored 3 months ago
  bcb1166b
- update reference commit · 3c782ce6
  Workum, Dirk-Jan van authored 3 months ago
  
  3c782ce6
- Merge branch 'develop' into update_reference_commit_vcf_change · 7082f1f3
  Workum, Dirk-Jan van authored 3 months ago
  
  7082f1f3
- Merge branch 'ensure_variants_msa_are_consistent' into 'develop' · 41987f93
  Workum, Dirk-Jan van authored 3 months ago
  41987f93
Apr 22, 2025
- fix the order of writing MSA variants by ordering them by 'id' · 89ff8320
  Workum, Dirk-Jan van authored 3 months ago
  
  89ff8320
- update reference commit for end-to-end test · ae8f46c4
  Workum, Dirk-Jan van authored 3 months ago
  
  ae8f46c4
- Merge branch 'add_check_for_sequences_in_vcf' into 'develop' · c7ad1b35
  Workum, Dirk-Jan van authored 3 months ago
  c7ad1b35
- ensure correct fasta headers are used to check against for VCF validation · 52a5a1c5
  Workum, Dirk-Jan van authored 3 months ago
  
  52a5a1c5
Apr 18, 2025
- update statement on how to update phenotype data in pangenome in documentation · b7b3fa84
  Workum, Dirk-Jan van authored 3 months ago
  
  b7b3fa84
Apr 17, 2025
- refactor checking sequence names in vcf · c83c40f7
  Workum, Dirk-Jan van authored 3 months ago
  
  c83c40f7
- Updated logging and creation of info files to give more nuance about how gaps where calculated · 7f2d4f6f
  Flege, Patrick authored 3 months ago
  
  7f2d4f6f
Apr 16, 2025
- Added more logging · 8aef3ae9
  Flege, Patrick authored 3 months ago
  
  8aef3ae9
- Added more logging · 31a6ccf6
  Flege, Patrick authored 3 months ago
  
  31a6ccf6
- accidentally removed the exception · dbf6663b
  Workum, Dirk-Jan van authored 3 months ago
  
  dbf6663b
- log all problematic sequences of VCF · c79ac00b
  Workum, Dirk-Jan van authored 3 months ago
  
  c79ac00b
- update changelog · 05d139db
  Workum, Dirk-Jan van authored 3 months ago
  
  05d139db
- add more logging to identify what sequence is the problem · 7ad43092
  Workum, Dirk-Jan van authored 3 months ago
  
  7ad43092
- Added loggin to test which nucleotides are removed · 9779c7e9
  Flege, Patrick authored 3 months ago
  
  9779c7e9
- add check for sequences of vcf to be present in pangenome · eab49ebc
  Workum, Dirk-Jan van authored 3 months ago
  
  eab49ebc
Apr 15, 2025
- Added default value for alignmentTHreshold in constructor · 8023d601
  Flege, Patrick authored 3 months ago
  
  8023d601