This commit introduces significant changes to the sequence processing pipeline, implementing parallel loading, k-mer budget control, explicit memory management, and refined logic for pair evaluation and resolution.
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 logic for handling embedded taxonomy, allowing users to specify taxonomy or extract it from sequences, while optimizing performance through reduced memory usage. It also adds batch reordering capabilities and implements comprehensive testing to ensure correct precedence rules and robust error handling for missing taxonomic paths.
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 change introduces the `obiprimers` command-line tool and a complete search pipeline for identifying primer pairs. It includes new data structures for pair evaluation, comprehensive search configuration options, and detailed CSV output handling for results.
Corrects the indexing strategy for seed searching, improving performance and introducing a new seed index structure for efficient pattern lookup.
This commit updates the core matching logic by shifting the indexing strategy to use two halves of k/2 bases, resulting in significant speed improvements for sequence matching. It also introduces a new `seedIndex` structure for fast pattern retrieval and implements comprehensive performance testing logic for matching functions. Future features, such as bit-parallel search, are deferred.
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