This commit introduces new constraints for kmer size and minimizer selection, defines super-kmers, and adds extensive new command-line options for filtering, conversion, merging, and packing indices. Documentation across the codebase has also been updated.
Implement advanced indexing architecture and query features
Introduces a partitioned, NUMA-aware indexing system, supports kmer filtering, evidence conversion, index packing, and advanced query capabilities including estimation and phylogenetic analysis.
Eric Coissac