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 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.
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.
Eric Coissac