Feature/sequence typer

[apetkau]

• Implements Implement a SequenceTyper #75 by adding a SequenceTyper class
• Partially implements a method to type SARS-CoV-2 genomes by their constellations of mutations (this still has bugs which is why I named the class ExperimentalSARSCov2ConstellationsTyper).
  • On some test data I've found typing Delta and a number of other variants works properly, but B.1.1.7/Alpha does not work due to differences in naming standards of mutations (HGVS: S:p.Y145del vs. constellations: s:Y144-).
  • Plus, with the way I'm generating VCF files, some MNP mutations are split across multiple VCF lines as SNPs, which leads to incorrect predictions by snpEff for the amino acid change (this also impacts B.1.1.7).
  • However, despite all these issues, I'm still merging this in now and leaving it as an Experimental class, which can be fixed up later.