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.
This update introduces the core clustering algorithm, including parallel execution, dynamic block sizing, and SIMD-accelerated scoring methods. It also adds robust sequence preparation, k-mer analysis, and comprehensive test data fixtures for validation.
Eric Coissac