Add reference sequence

[jeromekelleher]

Using fasta from e.g. here: https://github.com/nextstrain/nextclade_data/blob/release/data/datasets/sars-cov-2/references/MN908947/versions/2022-10-27T12:00:00Z/files/reference.fasta

[jeromekelleher]

Don't add the actual sequence though, because this would lead to ts.alignments() doing the wrong thing. Better to pad with Ns for things we've deliberately left out as wonky.

[jeromekelleher]

Have just added in the reference sequence formally. It seems less likely to cause problems to give the full alignments with the reference, than to give Ns for all non-variable sites.