Add the ComputeMSA module#230

Merged

rfm-targa merged 10 commits intomasterfrom

Dec 4, 2025

Commits on Sep 3, 2025

feat(ComputeMSA): add the ComputeMSA module to compute MSAs from allele calling results.
rfm-targa
committed

Commits on Sep 4, 2025

feat(ComputeMSA): add computations of protein and DNA MSAs containing only the variable positions.
rfm-targa
committed
feat(ComputeMSA): start adding options to ignore and/or exclude loci/positions if there are gaps or ambiguous bases. Remove $ from template commands in docs to allow users to copy and run commands …
rfm-targa
committed
feat(ComputeMSA): add options to exclude or ignore variable positions if any of the sequences has gaps or ambiguous characters. Add option to provide custom options to run MAFFT.
rfm-targa
committed

Commits on Sep 18, 2025

Commits on Nov 7, 2025

feat(ComputeMSA): added multiprocessing to multiple steps. Using SeqIO.index_db to store record information as a file on disk and to allow using the index with multiprocessing by efficiently loadin…
rfm-targa
committed

Commits on Nov 10, 2025

feat(SchemaEvaluator): the SchemaEvaluator module uses the ComputeMSA module to compute the loci MSAs.
rfm-targa
committed

Commits on Dec 4, 2025