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.
Eric Coissac