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  • add-logging
  • add-phenotype-to-consensus-tree
  • add-progress-bars
  • add-scoring-matrices-to-resources
  • add_RG_option
  • add_gfa_build_pangenome
  • add_gfa_export
  • add_loading_bars
  • add_panva_queries
  • add_promoter_sequence_analysis
  • add_wgs_roi
  • automatic_skip_core_phylogeny_fix
  • develop protected
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  • feature/fix-msa-with-threshold
  • feature/update-msa-with-aa-presence-threshold
  • fix-core-phylogeny-mode
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Created with Raphaël 2.2.030Aug29282523211615141121Jul20181714131130Jun292823221917161513129865230May2322191716151211108543228Apr26252423212019181413118765432131Mar3029282725242322212017161514131097632127Feb242322212017161514131076331Jan30272418131211remove unused codeUPDATE TO java 17 AND neo4j 5.11.0normalise database path and add logging to check content of databaseMerge branch 'develop' into update_dependencies_pantoolsupdate changelogMerge branch 'develop' into fix_functions_documentationmake --mode for remove_functions an optional parameter with default 'all'Merge branch 'fix_group_info_signalp' into 'develop'Merge branch 'develop' into fix_group_info_signalpupdate changelogMerge branch 'kmc_use_threads' into 'develop'Kmc now uses threads instead of coresupdating some variable naming according to conventionrenamed some packagesMoved build_panproteome from ProteomeLayer.java into build_panproteome package. Renamed ProteomeLayer.java to Grouping.java.Extracted read mapping functions from GenomeLayer class, moved into separate read_mapping package within analysis. Moved remaining classes to construction package.Removed duplicate (and wrong) package importMoved add_antismash and add_functions out of FunctionalAnnotations.java into `construction` package. Moved remaining functional annotation related functions into `analysis` package and renamed FunctionalAnnotations.java into FunctionalAnalysis.java.fixed bug g=caused by incorrect package pathsSplit `add_phenotypes` and `remove_phenotypes` commands from Classification.java into new `phenotypes` package. Moved remaining `classification` package into `analysis` package and `phenotype` package in `construction` package.Merge branch 'develop' of https://git.wur.nl/bioinformatics/pantools into phased_pangenomicsrefactor group_info to prevent proteome/genome clashes and fix signalp typoupdating the way remove_functions works in readthedocsMerge branch 'fix_group_info_documentation' into 'develop'fix the way groups are called with the -H argument in the documentationadded packages for "construction" and "analysis" in which most classes are to be divided for project readability purposes.Merge branch 'fix_workflow_panproteome_kmer_classification' into 'develop'Merge branch 'update_cicd_reference_commit_again' into 'develop'update reference commit CI/CD because of merge request !186Merge branch 'fix_trimming_count_msa' into 'develop'simplify trimSequences() even more to make the code readableupdate changelogremove multiplier by 3 and simplify trimSequence() method in MSA classMerge branch 'fix_documentation_msa_phenotype' into 'develop'make clear in documentation that phenotype for msa is a boolean and not taking any stringsremove kmer_classification from panproteome workflow as this is not possibleRenamed java classes and restructured them in smaller packages according to shared code.kmc now uses given threads instead of % cores, added --threads option to add_genomesMerge branch 'merge_phased_with_develop' into 'phased_pangenomics'Merge branch 'develop' of https://git.wur.nl/bioinformatics/pantools into merge_phased_with_develop