Push lrwmyplxxzkn #19

2026-06-09T08:28:14Z

coissac commented

2026-06-09 08:28:14 +00:00

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coissac added 4 commits 2026-06-09 08:28:15 +00:00

feat: add --head and --presence-threshold to dump and distance d626d42ec7

Introduces `--head N` to the `dump` command for early iteration termination and `--presence-threshold N` to the `distance` command for Jaccard filtering on count indexes. Updates filter defaults to adapt based on explicit ingroup/outgroup declarations. Fixes a Rust type mismatch in the unitig closure and updates partition iteration callbacks to return `bool` for proper early termination support. Documentation is updated accordingly.

Parallelize partition iteration using Rayon 2465cfbc4b

Introduce thread-local `Vec<u8>` buffers to eliminate concurrent I/O contention. Replace the mutable row counter with an `AtomicUsize` and `fetch_update` to enable lock-free early termination when the limit is reached. Collected chunks are then written sequentially to preserve partition ordering.

refactor: centralize k-mer filtering logic and add validation ce45e2fbe1

Refactor shared `FilterArgs` and `build_group_filter` to return a `Result` with explicit validation for fraction bounds, min/max ordering, and count constraints. Update conditional defaults for `--min-frac` and `--max-outgroup-count` to depend on explicit quorum flags, preventing silent configuration conflicts. Update documentation and MkDocs navigation to reflect the new centralized k-mer filtering system across `rebuild`, `dump`, and `unitig` commands.

docs: document conservative rounding strategy for filtering thresholds 7dd8db1409

Specifies that minimum bounds use ceiling and maximum bounds use floor to enforce strictness. Clarifies that the implementation avoids explicit rounding by directly comparing integer counts against floating-point fractions, which is mathematically equivalent.

coissac merged commit f65ecd19cc into main

2026-06-09 08:28:21 +00:00

coissac deleted branch push-lrwmyplxxzkn

2026-06-09 08:28:21 +00:00

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Reference: OBIKmers/obikmer#19