Push tklvqnrqtzpo #10

2026-05-26T15:40:58Z

coissac commented

2026-05-26 15:40:58 +00:00

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coissac added 6 commits 2026-05-26 15:40:59 +00:00

refactor: switch indexing to IndexMode and update metadata 7501b6e854

Replace EvidenceKind with IndexMode (Exact, Approx, Hybrid) across layer construction and query dispatch. Update PartitionMeta and LayerMeta serialization to centralize index-wide configuration. Add flexible push_layer overloads to LayeredMap for dynamic index expansion without full rebuilds. Improve UnitigFileReader to gracefully fallback to sequential scanning when indexes are missing, eliminating panics.

feat: centralize index configuration and add hybrid mode 98c14aade9

Centralizes index configuration by storing a single `IndexMode` (`Exact`, `Approx`, or `Hybrid`) in `PartitionMeta`, eliminating per-layer metadata files. Introduces a `Hybrid` evidence mode and an `--approx` CLI flag to toggle between exact and probabilistic indexing. Refactors the build and query pipelines to dynamically dispatch based on the configured mode, deferring `.idx` generation to Pass 2 and only requiring it for Exact/Hybrid modes. Updates layer opening to load appropriate data structures, enforces strict parameter validation during merges, and clarifies performance trade-offs in documentation.

Enforce minimum input paths and handle stdin sentinel 9e60a711bc

Update CLI validation to require at least 10 input paths, defaulting to stdin (`-`) when the argument list is empty. Refactor the path iterator to explicitly recognize the stdin sentinel, bypassing extension validation and directory expansion to ensure direct passthrough to the file buffer without triggering `stat()` or recursive traversal.

feat: add utils subcommand for renaming genome labels dfa0b2bac2

Introduces a `utils` CLI subcommand to enable in-place genome label renaming without full reindexing. Adds strict label validation to reject empty strings, filesystem separators, and control characters, ensuring safe CSV serialization. Updates index metadata, renames corresponding spectrum JSON files, and registers the command in the main dispatch logic. CLI reference documentation is also updated.

refactor: add rolling buffer methods and document label constraints 26ab165807

Added `is_empty()`, `clear()`, and `iter()` methods to the rolling statistics buffer to enable standard traversal and state reset operations. Documented genome label constraints, specifying forbidden characters, empty label rejection, space quoting requirements, and auto-derived label bypass rules. Additionally, updated doc comments and added `#[allow(dead_code)]` attributes for `kmer_offset` and `n_kmers` fields to suppress compiler warnings while reserving them for future `--detail` coverage vector logic.

feat: add Findere z-window filtering and detail mode coverage tracking 694da5208e

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.

coissac merged commit 82ec6aa1cf into main

2026-05-26 15:41:06 +00:00

coissac deleted branch push-tklvqnrqtzpo

2026-05-26 15:41:06 +00:00

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Reference: OBIKmers/obikmer#10