Push lsqnpxrxuvpp #62

2026-08-11T09:09:14Z

coissac commented

2026-08-11 09:09:14 +00:00

No description provided.

coissac added 8 commits 2026-08-11 09:09:15 +00:00

feat: add Mash distance metric and rolling entropy support 2610a4af79

Implement the Mash distance metric across the CLI, index, and compact vector traits. This includes adding a `Mash` variant to the `DistanceMetric` enum and `MetricArg` CLI argument, implementing the conversion from Jaccard distances using the standard mutation-rate estimator formula, and updating documentation with supported metrics and algorithmic references. Additionally, add an `entropy` method to rolling statistics for computing order-specific entropy.

docs: add central-position SNP distance estimator spec 45df9919e5

Introduces a design specification for inferring substitution rates directly from k-mers with conserved flanks. The document details a memory-efficient implementation that computes 4x4 base-pair tallies using existing MPHF structures, enabling classical corrections without de Bruijn graph materialization. Updates MkDocs navigation to include the new theory page.

feat: support negative count filters as group size offsets 8bc6d533e5

Updates CLI parsing to accept negative integers for count filters, interpreting them as offsets from the group size (e.g., `-1` means all but one). A resolution closure enforces a floor of 1 to prevent unconstrained filtering on small groups. Additionally, refines evolutionary distance documentation to condition comparisons on local homology, replacing union-based Jaccard with a self-contained `SnpTally`. This unified approach streamlines SNP and shared count computation, incorporates paralogy and heterozygosity handling, and enables direct derivation of corrected distance matrices without external dependencies.

feat: implement per-k-mer sibling counts and central neighbor generation ea914bb536

Introduce the siblingannex module in obicompactvec to store per-slot minorant flags and sibling counts in a memory-mapped annex file. Add a scatter-gather pipeline in obikindex to compute these values across index layers and write them to .psib files. Implement central_canonical_neighbors in obikseq for generating strand-aware k-mer variants around the middle base. Expose rolling statistics in obiskbuilder and update dependency graphs accordingly.

feat: add obipipeline for concurrent sibling annex stats ba990a48a0

Add the `obipipeline` crate and replace sequential scatter/gather logic with a concurrent pipeline using `Flat` and `Transform` stages. Introduce `SiblingAnnexStats` API to compute distributions, and add CLI flags to `distance.rs` for constructing the annex and exporting statistics as CSV.

Refactor k-mer sibling tracking to compact bitmask and on-demand counts 1a470eab9e

Replaces the explicit `SiblingInfo` struct and 3-bit minorant flags with a derived 4-bit presence mask (`FamilyMask`) that tracks observed bases per family. This eliminates redundant file I/O overhead by introducing a `PartitionCache` for batch lookups, simplifies serialization, and updates all downstream builders, stats computation, and tests to operate on the new bitmask representation. Adjusts CLI output to report deduplicated family sizes instead of histograms, ignores generated CSV files, and updates documentation to reflect the fixed canonical reference and new theory.

feat: add raw SNP distance calculation and CLI flag 49f329edd5

Exposes RawSnpDistanceOutput and implements KmerIndex::raw_snp_distance() to compute pairwise single-copy locus counts under a paralogy-aware rule. The implementation leverages ndarray for parallel matrix aggregation, producing raw p-distance matrices for sanity-checking. A --raw-snp-distance CLI flag is added to export results as CSV, mapping zero-eligible pairs to NA.

feat: add multi-genome SNP pseudo-alignment and CLI export

Release / create-release (push) Successful in 5m58s

Details

Release / build-macos-arm64 (push) Successful in 2m47s

Details

Release / build-linux-x86_64 (push) Successful in 8m50s

Details

CI / build (pull_request) Canceled after 5m42s

Details

f5e508ed33

Introduces a `SnpAlignment` struct and helper methods to construct per-genome SNP pseudo-alignments from sibling k-mer data, filtering monomorphic families and encoding bases as IUPAC ambiguity codes. Exposes the type at the crate root for simplified imports. Adds a `--snp` CLI flag to compute and export these alignments as an IUPAC-coded FASTA file. Updates theory documentation to propose a multi-genome framing approach for joint phylogenetic inference, resolving pairwise correspondence ambiguities through positional homology and partial coverage thresholds. Bumps crate version to 1.1.40.

coissac merged commit 2e7cfc4368 into main

2026-08-11 09:09:24 +00:00

coissac deleted branch push-lsqnpxrxuvpp

2026-08-11 09:09:24 +00:00

Sign in to join this conversation.

1 Participants

Notifications

Due Date

No due date set.

Dependencies

No dependencies set.

Reference: OBIKmers/obikmer#62