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25 Open 171 Closed
25 Open 171 Closed
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Issues list

Add flanking_deletions_as_missing flag enhancement New feature or request
#461 opened Dec 18, 2024 by jeromekelleher
1
Add support for reading raw MAFFT alignments
#460 opened Dec 18, 2024 by jeromekelleher
1
Add support for "description" for metadata fields
#459 opened Dec 18, 2024 by jeromekelleher
Update/remove tally lineages
#447 opened Dec 13, 2024 by jeromekelleher
Add ruff linting
#446 opened Dec 13, 2024 by jeromekelleher
Remove plot_subgraph
#445 opened Dec 13, 2024 by jeromekelleher
2
Add some prints at the start of infer
#442 opened Dec 12, 2024 by jeromekelleher
Document infer command and toml format
#439 opened Dec 12, 2024 by jeromekelleher
Replace node report Markdown with Panel
#437 opened Dec 8, 2024 by jeromekelleher
Cleaup node_report header
#435 opened Dec 7, 2024 by jeromekelleher
Cannot convert numpy types to json (numpy 2.0)
#433 opened Dec 4, 2024 by hyanwong
Future work: weighting HMM matching by mutational probability
#431 opened Dec 4, 2024 by hyanwong
2
Fix imports to exclude optional "info" module
#373 opened Oct 17, 2024 by jeromekelleher 1.0
Alternative approach to encoding deletions
#367 opened Oct 14, 2024 by hyanwong
Quantify how well we pick up saltational variants
#337 opened Oct 7, 2024 by szhan
7
Fix earliest_date for unknown lineages
#303 opened Sep 25, 2024 by jeromekelleher 1.0
Add TreeInfo tool to report on retrospective matches
#296 opened Sep 24, 2024 by jeromekelleher 1.0
No "match_info" field when calling combine_recombinant_info
#285 opened Sep 19, 2024 by hyanwong
5
Fix and test TreeInfo
#271 opened Sep 13, 2024 by jeromekelleher 1.0
Remove 0 and L from recombinant breakpoints bug Something isn't working
#161 opened May 16, 2023 by jeromekelleher
pango_recombinant_lineages_report is misleading
#111 opened Mar 3, 2023 by jeromekelleher
Classification for non-biological reversions
#100 opened Feb 12, 2023 by jeromekelleher
13
Add site_summary data frame
#98 opened Feb 10, 2023 by jeromekelleher
1
Classifying reversion mutations
#94 opened Feb 8, 2023 by hyanwong
1
Reversion push code needs to deal with recombinants
#86 opened Feb 6, 2023 by jeromekelleher
2
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