v3.0.0 Major refactoring and new features

New Features

• Sample input file can either be in FASTA format (together with reference sequence), as it used to be in previous versions, or a csv table containing a data and dna profile akin to the output table of a covSonar database.
• If reported cases are available, calculate and plot the minimum number of infected individuals

Other changes

• Refactoring and deleting unused artefacts in the code
• Normalise parameter for phi estimation by days spanning the bin
• Kernel smoothing instead of resampling
• Change optimizer to Nelder-Mead instead of
• Intermediate results are temporary (before they were saved)
• R0 estimation is not available anymore
• Masking positions directly with position intervals and not vcf file anymore
• No binning by week (can be set by days_per_bin=[7,..] and no percentage, i.e. number of sequences have to be set in order to be considered
• Adjusted parameter names and new parameters in config.yaml (described in the README)