5 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	4fc7860825	feat: filter zero-valued entries from kmer strict matches output ... Optimize query serialization by conditionally excluding genomes with zero total matches. This reduces JSON payload size while preserving the label-to-count mapping structure. Updates architecture documentation and bumps version to 1.1.36.	2026-07-07 10:50:01 +02:00
Eric Coissac	8a0b898b4b	docs: clarify query pipeline, Findere trick, and input formats ... Fix a stray prefix in the README heading and update documentation to reflect the query pipeline's operation on `s-mers` (`s = k - z + 1`) with post-partition z-window filtering. Clarify the Findere trick, including k-mer size reduction, consecutive match requirements, and false positive rate calculations. Additionally, expand input format documentation to cover supported file extensions, gzip compression, recursive directory handling, and `query` command specifications.	2026-05-30 15:59:12 +02:00
Eric Coissac	694da5208e	feat: add Findere z-window filtering and detail mode coverage tracking ... Introduces the `--findere-z` CLI flag to override the index's sliding window parameter and implements `apply_findere` to filter k-mer hits using a z-consecutive positions window. Adds structural support for `--detail` mode, including per-sequence k-mer offsets, conditional allocation of per-position coverage vectors, and JSON serialization. Updates architecture documentation, CLI references, and annotation schemas to align with the new implementation, resolving prior discrepancies with `--detail` and `--mismatch` flags.	2026-05-26 15:43:17 +02:00
Eric Coissac	036d044291	refactor: update core types and add approximate evidence support ... Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.	2026-05-26 10:04:25 +02:00
Eric Coissac	13599dd444	feat: Implement query subcommand for sequence-to-genome mapping ... This change introduces the `query` CLI command and its supporting infrastructure for sequence-to-genome mapping and k-mer matching. It adds a `QueryLayer` abstraction backed by MPHF and persistent matrices, exposes the index partition for direct querying, and implements `Hash`/`Eq` for `RoutableSuperKmer`. The command ingests sequence batches, deduplicates superkmers, routes them to index partitions for parallel exact or 1-mismatch matching, and outputs results as FASTA records annotated with JSON metadata. Includes `serde_json` dependency addition, module exports, and documentation updates.	2026-05-21 18:56:41 +02:00