Add option to keep synonymous at 1 for multi

[FerriolCalvet]

Model synonymous with the multi approach but not using all the ALTREADS, but counting them only once. We would still use the alt reads for the impactful mutations.

Be careful with this, but at least give the possibility.

[FerriolCalvet]

When implementing this, think if it is worth it to add some intermediate option where the user can choose something in between all the observed synonymous mutated reads and 1 mutated read per mutation