Refactor Kmer indexing and add phylogenetic analysis features
This commit introduces a complete overhaul of the Kmer indexing architecture, including new support for 2-bit encoding, canonical super-kmer handling, and a partitioned processing pipeline. Additionally, it adds comprehensive phylogenetic capabilities, including multiple distance metrics, SNP correction models, and models for rate heterogeneity and sampling design.
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.
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Refine indexing architecture and command usage documentation
Updates the core documentation for kmer structure, super-kmer routing, and indexing layout. Introduces new command-line options for filtering, dumping, and conversion, clarifying the Exact/Approx trade-offs and constraints for sequence processing.
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