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Releases: cbg-ethz/cojac

Version 0.9.3 - tables for LolliPop

27 Nov 11:24
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preview feature:

  • produce tables that can be used for LolliPop

    • tabmut: --add-mutations — add mutations strings to tabmut

      Necessary for using "bootstrapping" confidence intervals in LolliPop

    • cooc-mutbamscan: --fix-subsets — subset of coocurring 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 mutations A and B
      amplicon with mutations A and B is flagged to both var 1 and 2

      Useful for, e.g., delta and early omicron waves.

Version 0.9.2 - LAPIS improvement

03 Jun 22:42
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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

04 Sep 14:39
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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

29 Mar 15:10
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  • 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