Uncertain stop codon in protein descriptions (fs and ext)
When a variant results in a frame shift or extension and we don't
see a new stop codon in the RNA, the protein description should use
the notation for an uncertain stop codon, e.g., p.(Gln730Profs*?)
instead of p.(Gln730Profs*96) where 96 is just the last codon in
our transcript [1].
To detect this, we now use to_stop=False in our .translate()
calls, since that will explicitely return * characters for stop
codons.
We also slightly fix the coloring of changes in the protein sequence where previously changed stop codon characters where not included.