Releases: cbg-ethz/cojac
Releases · cbg-ethz/cojac
Version 0.9.3 - tables for LolliPop
preview feature:
-
produce tables that can be used for LolliPop
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tabmut
:--add-mutations
— add mutations strings to tabmutNecessary for using "bootstrapping" confidence intervals in LolliPop
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cooc-mutbamscan
:--fix-subsets
— subset of coocurring mutationsFix variants attribution when cooccurrence are subset/superset of other variants:
if var 1 has mutations A, B and C and var 2 has mutations A and B
amplicon with mutations A and B is flagged to both var 1 and 2Useful for, e.g., delta and early omicron waves.
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Version 0.9.2 - LAPIS improvement
Bugfixes and improvement for sig generation from GeneSpectrum:
- support LAPIS v2
- switch to lineage field
- quirk field to workaround bugs in servers
Preview feature:
- alpha importer from NextStrain
Version 0.9.1
Bug fixes:
--url
was broken insig-generate
andcooc-curate
New features:
- sort BED file by position, on by default
(avoids wrong amplicons names in out-of-order file) - comment amplicons query file, on by default
(add comments such as# SARS-CoV-2_25_RIGHT
)- helps double check amplicon names
- simplify searching for primers affected by mutation
by (ab)using COJAC's cooc-mutbamscan and primer BED files
Version 0.9
- Converted to a proper python package with poewtry and click
- Command format has changed
- Integrated into V-pipe
- Tool for generating list of mutations from Cov-Spectrum to be used in
creating COJAC's specific YAML files - Select API end-point on Cov-Spectrum (ENA or GISAID)
- Accesskey for non-open (GISAID) on Cov-Spectrum
- Tool for converting list of mutations from TSV on Covariants.org repo
- Partial support for aarch64
- pysam still missing on bioconda
Publication:
- change of literature ref to Nature Microbiology
- Notebooks used in publication more portable