Merge requests · bioinformatics / PanTools

New phenotype msa output 5 of 5 checklist items completed

!145 · created Mar 22, 2023 by Jonkheer, Eef develop
- Merged
- 113
- Approved
updated Aug 15, 2023
Move graph and bean validation to utils

!144 · created Mar 21, 2023 by Robin van Esch include_variation
- Merged
- 9
- Approved
updated Mar 30, 2023
Moved from general constraint validators for msa to a specific msa validator

!143 · created Mar 20, 2023 by Robin van Esch fix_msa_alignment_type
- Merged
- 7
- Approved
updated Mar 23, 2023
Change default input sequence type behavior for MSA

!142 · created Mar 20, 2023 by Workum, Dirk-Jan van develop
- Merged
- 9
- Approved
updated Aug 15, 2023
refactored add_variants, add_pav, remove_variants, remove_pav and variation_overview 6 of 6 checklist items completed

!141 · created Mar 14, 2023 by Robin van Esch include_variation
enhancement
- Merged
- 49
- Approved
updated Mar 17, 2023
Fix maven compile warnings

!140 · created Mar 14, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Mar 16, 2023
Fix automatic skipping of genomes in core phylogeny

!139 · created Mar 09, 2023 by Jonkheer, Eef develop
- Closed
updated Mar 11, 2023
Reduce logging build pangenome

!138 · created Mar 03, 2023 by Robin van Esch develop
- Merged
- Approved
updated Mar 15, 2023
Moving busco_protein out of classification

!137 · created Mar 02, 2023 by Jonkheer, Eef develop
- Closed
- 25
updated Mar 11, 2023
fixing linking of mRNA node from non-standard GFF with functional annotation

!136 · created Feb 23, 2023 by Pardeshi, Lakhansing develop
- Merged
- 3
- Approved
updated Feb 24, 2023
Update conda environments

!135 · created Feb 17, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Feb 23, 2023
Fix backwards compatibility MSA

!134 · created Feb 16, 2023 by Workum, Dirk-Jan van develop
- Merged
- 5
- Approved
updated Mar 14, 2023
Reformatted AnnotationLayer.addAnnotations

!133 · created Feb 13, 2023 by Robin van Esch develop
- Merged
- 30
updated Apr 25, 2023
Fix adding annotations with missing mRNAs 1 of 1 checklist item completed

!132 · created Feb 10, 2023 by Workum, Dirk-Jan van develop
- Merged
- 10
- Approved
updated Feb 21, 2023
Remove last jar files from code base

!131 · created Feb 10, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Feb 17, 2023
Fix typos in core_phylogeny that mixed up genes and groups

!130 · created Feb 07, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Feb 07, 2023
Change functional database parameter for add_functions 2 of 2 checklist items completed

!129 · created Feb 03, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Feb 06, 2023
Add variation (SNPs, InDels and PAVs) to PanTools 7 of 7 checklist items completed

!128 · created Jan 30, 2023 by Workum, Dirk-Jan van develop
- Merged
- 53
updated Mar 30, 2023
Merge v4.1.1 changes to develop

!127 · created Jan 30, 2023 by Workum, Dirk-Jan van develop
updated Jan 30, 2023
Release PanTools v4.1.1

!126 · created Jan 27, 2023 by Workum, Dirk-Jan van
- Merged
- Approved
updated Jan 30, 2023