Merge requests · bioinformatics / PanTools · GitLab

Update pantools version to 4.2.1

!162 · created Jun 02, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Jun 05, 2023
Add badges to README

!115 · created Jan 04, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Jun 02, 2023
Update readthedocs documentation 6 of 6 checklist items completed

!160 · created May 15, 2023 by Workum, Dirk-Jan van develop
- Merged
- 2
- Approved
updated Jun 02, 2023
Fix default settings for 'pantools group'

!161 · created May 22, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated May 22, 2023
Fix protein specific FastTree option

!157 · created May 08, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated May 22, 2023
Add check whether bcftools and tabix exist before running add_variants

!159 · created May 08, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated May 22, 2023
Changes from v4.2.0 to develop

!156 · created May 08, 2023 by Workum, Dirk-Jan van develop
updated May 08, 2023
Fix readthedocs.io documentation build

!155 · created May 08, 2023 by Workum, Dirk-Jan van
- Merged
- Approved
updated May 08, 2023
Merge release 4.2.0 into pantools_v4

!154 · created May 04, 2023 by Robin van Esch
- Merged
- Approved
updated May 08, 2023
Updated version number for new release 4.2.0

!153 · created May 04, 2023 by Robin van Esch develop
- Merged
- Approved
updated May 08, 2023
Fix "no such property, 'protein_ID'" for `pantools add_variants`

!152 · created Apr 28, 2023 by Workum, Dirk-Jan van develop
- Merged
- 1
- Approved
updated May 04, 2023
Fix filenames msa & core_phylogeny

!151 · created Apr 25, 2023 by Workum, Dirk-Jan van develop
- Merged
- Approved
updated Apr 28, 2023
Reformatted AnnotationLayer.addAnnotations

!133 · created Feb 13, 2023 by Robin van Esch develop
- Merged
- 30
updated Apr 25, 2023
Added `Pantools.logger` instead of `System.out.print*`

!149 · created Mar 30, 2023 by Ahmed, Nauman develop
enhancement
- Merged
- Approved
updated Apr 03, 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
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
Updated CLI for new functions.

!146 · created Mar 23, 2023 by Robin van Esch phased_pangenomics
updated Mar 25, 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
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

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