This change introduces the core functionality for identifying, validating, and statistically evaluating primer pairs within the corpus. It includes new data structures for primer parameters, amplicon statistics, and sequence handling, along with methods for assigning taxa to sequences. Comprehensive tests are added to ensure the accuracy of the pair evaluation against expected outputs.
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.
This change introduces thread-safe pipe registration and unregistration functions using `sync.WaitGroup` and `atomic.Int64` to manage the count of registered pipes, addressing a race condition identified by the race detector.
This introduces new structures for defining sequence roles and constraints, core logic for strict word identification, and comprehensive unit tests to ensure accuracy and correct behavior.
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