Update reference proteome analysis to consider patient genotype

Currently we compare peptide sequences against a reference proteome from Ensembl.

It would be more correct to create a proteome that incorporated SNPs that impact protein sequence and then look for matches between our peptide sequence and THAT personalized proteome reference.

We could take our germline VCF, use it to update a reference genome fasta with het/hom SNPs, extract CDS sequences based on all annotated protein coding transcripts from Ensembl and then build the peptide reference for comparison from that.

Start by tracing how the current Ensembl reference proteome is built and used for peptide matching. Then investigate how the germline VCF, reference genome FASTA, and annotated protein-coding transcripts could produce a genotype-specific proteome. Done means peptide comparisons use that personalized reference while handling heterozygous and homozygous protein-impacting SNPs.