This commit introduces refinements to primer design strategies, species identification rules, and performance analysis. It also updates taxonomy handling by implementing methods for setting and dropping taxonomic paths, along with necessary utility improvements for set handling and comprehensive test coverage.
This update introduces new configuration options for pair selection, including multi-match filtering, circularity settings, and reference site validation. It also enhances the search functionality to correctly identify and track repeated sequences and reference locations, improving the accuracy of primer pair identification.
This commit introduces the core matching functionality, including parallel corpus loading, the `Corpus` data structure, and implementations for `matchNaive` and `matchApat`. It also defines new matching rules, variant handling, and comprehensive unit and integration tests to validate the new logic and parameter handling.
Eric Coissac