Documentation for annotate_maf_triplet

[rdmorin]

I have some suggestions for how this functions documentation could be improved for clarity and completeness.

1. pyrimidine_collapse parameter is not explained. It just says "Estimate mutation_strand and"
2. fastaPath should start by saying what it is e.g. "the path to the genome fasta file corresponding to the genome build"
3. bsgenome_name: Please provide an actual worked example showing a name instead of just the explanation for how to construct the name.
4. ref and alt are ignored (I think) when all_SNVs is TRUE but this is not made clear.
5. projection: what is the purpose of this argument and how does it relate to the fastaPath and bsgenome_name (i.e. does one make the others unnecessary? Please specify so users don't have to figure this out themselves)

I also think the genome reference could be automatically found so is this parameter unnecessarily confusing? Or is that actually done already using the information in the MAF? In any case, the optional arguments need to be clarified so users don't assume that these need to be provided.