Version 0.9.3 - tables for LolliPop

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.