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artic-network
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civet
Cluster Investigation & Virus Epidemiology Tool
https://cov-lineages.org/resources/civet.html
GNU General Public License v3.0
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Error when preparing background data following guideline
#165
genomesurveillance
closed
1 year ago
10
adding checks for date col
#164
aineniamh
closed
2 years ago
0
patch for issues when sequence fails qc and tries to hit catchment
#163
aineniamh
closed
2 years ago
0
Background curation
#162
aineniamh
closed
2 years ago
0
gofasta dist-push error
#161
rjorton
closed
2 years ago
1
Background curation and accepts tsvs now
#160
aineniamh
closed
2 years ago
0
Time series figure
#159
aineniamh
closed
2 years ago
0
Time series figure
#158
aineniamh
closed
2 years ago
0
search for mutations of interest
#157
omarkr8
closed
2 years ago
1
global snipit pipeline broken
#156
aineniamh
closed
2 years ago
1
gofasta parsing breaks if all background data is in the query (or nearly all) because it is all supplied in the ignore file.
#155
aineniamh
opened
2 years ago
0
allow other date formats to be parsed
#154
aineniamh
closed
2 years ago
1
sample_dte shouldn't be needed if no timeline
#153
aineniamh
opened
2 years ago
0
turn the background tests back on- or at the very least check if the sequences are the same length
#152
aineniamh
opened
2 years ago
0
tree annotations defaults break if not there
#151
aineniamh
closed
2 years ago
1
`-bicol` option also overrides `-sicol` option
#150
rambaut
opened
2 years ago
1
snipit error, not sure how to debug
#149
omarkr8
opened
2 years ago
2
trees are too thin?
#148
omarkr8
closed
2 years ago
2
help with line 120 error?
#147
omarkr8
closed
2 years ago
1
Add catch for locations with no sequences for background mapping
#146
ViralVerity
closed
2 years ago
0
civet3 PR to ARTIC
#145
aineniamh
closed
2 years ago
0
Install error
#144
mabouelk
opened
2 years ago
3
link out tips in catchment trees to global tree?
#143
aineniamh
opened
2 years ago
0
Collapse local trees to polytomies in report
#142
aineniamh
opened
2 years ago
0
Make timeline colour by something as a dynamic option in the report
#141
ViralVerity
opened
2 years ago
0
Make highlight lineages an option in background map
#140
ViralVerity
opened
2 years ago
0
Make pies moveable in local lineages
#139
ViralVerity
opened
2 years ago
0
Switch for turning pie labels on and off in local lineages
#138
ViralVerity
closed
2 years ago
1
Make colours in background map consistent between pies
#137
ViralVerity
closed
2 years ago
1
Add in country to tooltips in local lins
#136
ViralVerity
closed
2 years ago
0
Other shows up in local lineages when it shouldn't
#135
ViralVerity
closed
2 years ago
0
ERROR: Alignment must have at least 3 sequences
#134
GonzaloYebra
opened
3 years ago
0
--sicol, --bcol, --icol interaction when some sequences are matched and some are provided
#133
ViralVerity
opened
3 years ago
0
Remove --centroid-file option and just work out centroids from custom input file
#132
ViralVerity
opened
3 years ago
0
--global_snipit to summarize diversity among all query sequences
#131
matt-sd-watson
closed
3 years ago
3
Collapse local trees for polytomys by default in the report
#130
aineniamh
opened
3 years ago
0
background data curation feature
#129
aineniamh
closed
3 years ago
3
snipit breaks if no changes from ref input into alignment
#128
aineniamh
opened
3 years ago
0
background downsample still included in tree 🙄
#127
aineniamh
closed
3 years ago
2
mutation label background in the tree
#126
aineniamh
closed
3 years ago
1
jquery table with dynamic column selection
#125
aineniamh
closed
3 years ago
1
mutation table usng scorpio
#124
aineniamh
closed
3 years ago
1
Toggle button to turn labels on/off in background map
#123
ViralVerity
closed
2 years ago
0
Grid lines and sorting for timelines
#122
ViralVerity
opened
3 years ago
0
Sort out zoom issues and starting arc size in background diversity maps
#121
ViralVerity
closed
2 years ago
0
Update docs for new tree building approach
#120
aineniamh
closed
3 years ago
0
Layer of env variables to look for
#119
aineniamh
opened
3 years ago
0
treemap section to the report with configurable column, default lineage
#118
aineniamh
opened
3 years ago
0
make it clearer which nodes are downsampled in the tree
#117
aineniamh
opened
3 years ago
0
Change internal strings to config.py variables globally defined
#116
aineniamh
opened
3 years ago
0
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