Tags

Version 0.9.3

preview feature:
- produce tables that can be used for LolliPop

  - tabmut: --add-mutations - add mutations strings to tabmut

    Necessary for using "bootstraping" confidence intervals in LolliPop

  - coocmutbamscan: --fix-subsets - subset of coocurrating mutations

    Fix variants attribution when cooccurrence are subset/superset of other variants:
    if var 1 has mutations A, B and C and var 2 has muations A and B
    amplicon with mutations A and B is flagged to both var 1 and 2

Version 0.9.2

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 in `sig-generate` and `cooc-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

Version 0.2

 - hard-coded table replaced with:
   - BED fields for amplicons regions
   - YAML for signatures / variants definition
   - amplicon query tables can themselve by saved and reused
 - tool for importing signatures from PHE-Genomics
 - (preliminary) tool for evaluating quality of variants definition
   using mutation prevalences fetched from CoV-Spectum

First bioconda package release