Introduces the SeqKmerCounter structure for parallel k-mer counting, refactors sequence reading and writing logic, and adds comprehensive test coverage for various sequence scenarios.
Introduces parallel processing for clustering, refines scoring mechanisms, and expands test coverage for the alignment functionality.
This change introduces parallel processing capabilities within the clustering logic, updates the core similarity engine with new data structures and scoring methods, and implements a comprehensive test suite for the alignment tool. It also adds new command-line options for configuring alignment parameters and reference lengths.
Eric Coissac