[ ] Bi-allelic metagenotypes can/should be encoded as ref/alt columns instead of a fully "flattened" format. (How should this be implemented?)
[ ] Add a --midas-metagenotype flag to app.Load that imports directly from midas2_output/merge/snps/${species}/${species}.{snps_depth,snps_freqs}.tsv.lz4 pairs.
Three refinements would make metagenotype TSV files more intuitive, less bloated, and safer:
Metagenotype.to_tsvmethod).--midas-metagenotypeflag toapp.Loadthat imports directly frommidas2_output/merge/snps/${species}/${species}.{snps_depth,snps_freqs}.tsv.lz4pairs.