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jeromekelleher
/
sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Add inference time plot
#334
jeromekelleher
closed
51 minutes ago
0
Don't store exact matches, keep a count
#333
jeromekelleher
closed
1 hour ago
0
Track deletions, and fix errors in missing tracking
#332
jeromekelleher
closed
10 hours ago
1
Counting genome-wide mutations above a focal node
#331
szhan
opened
10 hours ago
0
Track deletions per site, like missing data
#330
jeromekelleher
closed
10 hours ago
0
Non filtered samples getting lost
#329
jeromekelleher
closed
12 hours ago
1
Add causal pango to recombinants
#328
jeromekelleher
closed
12 hours ago
0
Basic working version of recombinants summary
#327
jeromekelleher
closed
1 day ago
0
Don't depend on new site metadata
#326
jeromekelleher
closed
2 days ago
0
Fix functions affected by changing site metadata missing_samples to masked_samples
#325
szhan
opened
2 days ago
1
Fix bug when accessing node metadata date_added
#324
szhan
closed
2 days ago
0
Don't store exact matches
#323
jeromekelleher
closed
1 hour ago
0
Turn off (or remove) window-based site masking
#322
szhan
closed
11 hours ago
2
Disregard excluded sites when computing base composition
#321
szhan
closed
3 days ago
4
Quick hack to turn off masking
#320
jeromekelleher
closed
3 days ago
2
Examine filtering based on total masked sites
#319
jeromekelleher
closed
11 hours ago
2
Fix skip date in run script
#318
szhan
closed
5 days ago
1
Skip date in run script
#317
szhan
closed
5 days ago
2
Quick hacky version hard-coding metadata filtering
#316
jeromekelleher
closed
3 days ago
0
Enable neighbour joining for sample group inference
#315
jeromekelleher
closed
1 week ago
0
Rerooting
#314
jeromekelleher
closed
1 week ago
21
Local tree around the emergence of Delta
#313
szhan
opened
1 week ago
4
Switch in biotite NJ algorithm for local tree building
#312
hyanwong
closed
1 week ago
13
Replacing UPGMA
#311
hyanwong
closed
1 week ago
4
Node flags not consistently set for nodes tagged with a group_id in metadata
#310
jeromekelleher
opened
1 week ago
0
Better lineage logging
#309
jeromekelleher
closed
1 week ago
0
Add parameter for min root mutations
#308
jeromekelleher
closed
1 week ago
0
Add "Country_abbrev" to node metadata
#307
hyanwong
closed
1 week ago
1
Add ability to label samples with metadata (e.g. Pangolin designation)
#306
hyanwong
closed
1 week ago
2
Lineage tools
#305
jeromekelleher
opened
1 week ago
0
Prettify sample_group draw_svg()
#304
hyanwong
closed
1 week ago
0
Fix earliest_date for unknown lineages
#303
jeromekelleher
opened
1 week ago
0
Pango lineage data
#302
jeromekelleher
closed
1 week ago
0
Update "Attach" log message to put variable length stuff at end
#301
jeromekelleher
closed
1 week ago
1
Add tally_lineages tool
#300
jeromekelleher
closed
1 week ago
0
Stricter filtering
#299
jeromekelleher
closed
1 week ago
0
Add info for several major VoCs
#298
szhan
closed
1 week ago
1
Improve viz and move attribute to properties where possible
#297
jeromekelleher
closed
1 week ago
0
Add TreeInfo tool to report on retrospective matches
#296
jeromekelleher
opened
1 week ago
0
Add CLI tool to compare number of samples for each pango lineage in metadata DB vs ARG
#295
jeromekelleher
closed
1 week ago
0
Initial debug data on groups
#294
jeromekelleher
closed
1 week ago
0
Improve retrospective group adding logs and top-level info
#293
jeromekelleher
closed
1 week ago
0
Initial clade info + group retrospectives by location
#292
jeromekelleher
closed
1 week ago
0
Add NODE_IS_RETROSPECTIVE_GROUP flag
#291
jeromekelleher
closed
1 week ago
0
Add data on major clades for QC
#290
jeromekelleher
closed
1 week ago
9
Add branch length plots to TreeInfo
#289
jeromekelleher
closed
1 week ago
0
Move recombinant processing offline
#288
jeromekelleher
closed
2 weeks ago
0
Progress labels not set for recombinant matching
#287
jeromekelleher
closed
1 week ago
0
Properly reference ArgRecombinant
#286
hyanwong
closed
2 weeks ago
0
No "match_info" field when calling `combine_recombinant_info`
#285
hyanwong
opened
2 weeks ago
5
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