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.
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.
Eric Coissac