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32 Open 96 Closed
32 Open 96 Closed
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Issues list

gofasta parsing breaks if all background data is in the query (or nearly all) because it is all supplied in the ignore file.
#155 opened Mar 8, 2022 by aineniamh
sample_dte shouldn't be needed if no timeline
#153 opened Mar 8, 2022 by aineniamh
turn the background tests back on- or at the very least check if the sequences are the same length
#152 opened Mar 8, 2022 by aineniamh
-bicol option also overrides -sicol option enhancement New feature or request
#150 opened Jan 31, 2022 by rambaut
1
snipit error, not sure how to debug
#149 opened Jan 17, 2022 by omarkr8
2
Install error
#144 opened Nov 22, 2021 by mabouelk
3
link out tips in catchment trees to global tree? enhancement New feature or request
#143 opened Oct 29, 2021 by aineniamh
Collapse local trees to polytomies in report enhancement New feature or request
#142 opened Oct 29, 2021 by aineniamh
Make timeline colour by something as a dynamic option in the report civet3 enhancement New feature or request
#141 opened Oct 27, 2021 by ViralVerity
@ViralVerity
Make highlight lineages an option in background map civet3 enhancement New feature or request
#140 opened Oct 12, 2021 by ViralVerity
Make pies moveable in local lineages civet3 enhancement New feature or request
#139 opened Oct 8, 2021 by ViralVerity
ERROR: Alignment must have at least 3 sequences bug Something isn't working
#134 opened Sep 29, 2021 by GonzaloYebra
--sicol, --bcol, --icol interaction when some sequences are matched and some are provided civet3
#133 opened Aug 25, 2021 by ViralVerity
Remove --centroid-file option and just work out centroids from custom input file civet3 enhancement New feature or request
#132 opened Aug 13, 2021 by ViralVerity
Collapse local trees for polytomys by default in the report civet3 enhancement New feature or request
#130 opened Aug 6, 2021 by aineniamh
snipit breaks if no changes from ref input into alignment bug Something isn't working civet3
#128 opened Jul 29, 2021 by aineniamh
Grid lines and sorting for timelines civet3 enhancement New feature or request
#122 opened Jul 28, 2021 by ViralVerity
Layer of env variables to look for civet3 enhancement New feature or request
#119 opened Jul 27, 2021 by aineniamh
treemap section to the report with configurable column, default lineage civet3 enhancement New feature or request
#118 opened Jul 27, 2021 by aineniamh
make it clearer which nodes are downsampled in the tree civet3 enhancement New feature or request
#117 opened Jul 27, 2021 by aineniamh
Change internal strings to config.py variables globally defined civet3 enhancement New feature or request
#116 opened Jul 27, 2021 by aineniamh
Speed up for background fasta file parsing- don't use biopython civet3 enhancement New feature or request
#114 opened Jul 16, 2021 by aineniamh
private columns as env variable, public flag for safe report civet3 enhancement New feature or request
#112 opened Jul 16, 2021 by aineniamh
full pipeline description docs civet3 documentation Improvements or additions to documentation
#108 opened Jul 15, 2021 by aineniamh
Feature: infer local catchment phylotypes civet3 enhancement New feature or request
#107 opened Jul 15, 2021 by aineniamh
ProTip! Exclude everything labeled bug with -label:bug.