Push ruqusmkoyvwm #16

2026-06-05T08:41:01Z

coissac commented

2026-06-05 08:41:01 +00:00

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coissac added 10 commits 2026-06-05 08:41:01 +00:00

feat: add metadata-driven k-mer filtering for rebuild command 476c7a6394

Introduces a metadata-driven filtering system for the rebuild command, classifying genomes into ingroup and outgroup categories using exact, inequality, and hierarchical path predicates. Implements a GroupQuorumFilter to enforce configurable presence thresholds and fraction constraints per group. Refactors the command to replace global quorum filters with this unified approach, converts the presence flag to a threshold parameter, and adds corresponding documentation and MkDocs navigation.

feat: add kmer filtering and refactor layer iteration a1499e6153

Introduce a `passes_all` utility to validate kmer rows against multiple filters using short-circuit logic. Integrate a `filters` parameter into the iteration functions to conditionally emit kmers based on filter results. Extract repetitive layer traversal and filtering into an `iter_src_layers` helper, refactoring Pass 1 and Pass 2 to eliminate duplication. Additionally, add a debug conditional to the dump output to include partition and layer metadata alongside kmer sequences.

feat: add selective k-mer filtering to dump and rebuild commands 3e62ffe010

Add the `obidebruinj` dependency and introduce `FilterArgs` CLI arguments for ingroup/outgroup predicates and count/fraction thresholds. Extend `GroupFilterParams` to support outgroup filtering, and integrate the filter collection into `KmerIndex::dump` and `rebuild` commands. This enables selective k-mer filtering during index operations and CSV exports.

refactor: replace unitig extraction with de Bruijn graph pipeline 712a03a3a6

This change replaces direct partition-based extraction with a pipeline that reconstructs a de Bruijn graph from filtered k-mers. It introduces `FilterArgs` for k-mer selection, collects filtered k-mers in parallel into a `GraphDeBruijn`, computes node degrees, and enumerates unitigs from the graph for output instead of reading pre-computed partition files.

perf: Replace manual window tracking with monotonic deque algorithm 9306ec1c56

Eliminates intermediate allocations by computing per-genome window minimums (`win_min`) directly. Unifies the `z ≤ 1` and `z > 1` branches into a single buffer-reused accumulation loop, efficiently validating k-mer presence.

docs: expand kmer indexing, filtering, and merging documentation bb7adc1154

Expands MkDocs navigation and documentation for evidence elimination, the merge command, and kmer filtering. Refactors kmer representation to a generic `KmerOf<L>` type with a bitwise reverse complement algorithm. Unifies MPHF construction, introduces approximate fingerprint-based indexing, and updates the pipeline, chunkreader, and storage layouts. Adds code coverage reports and clarifies architectural invariants for improved maintainability.

feat: add bits-per-kmer diagnostic and stats module edd5e3f8ee

Introduce a `stats` module to compute normalized storage efficiency metrics. The new `KmerIndex::bits_per_kmer()` method parallelizes disk I/O across partitions to aggregate file sizes for MPHF, evidence, and matrix components. Publicly export `IndexBitsPerKmer` and add a `--bits-per-kmer` CLI flag to trigger the diagnostic routine and print detailed statistics.

feat: Add parallel execution and thread-safe graph operations 2f29ee2240

Integrate rayon to enable parallel processing of k-mer partitions and degree computation. Replace Cell with AtomicU8 to ensure thread-safe node state management, and add a merge method for combining disjoint graphs. Additionally, introduce progress tracking utilities and a test-utils feature flag for development dependencies.

perf: add structured performance profiling for unitig stages 249998beed

Wraps graph construction, degree computation, and unitig enumeration phases with `Stage` start/stop calls. Intervals are recorded in a `Reporter` instance and printed upon completion to provide granular timing metrics for each computational stage.

feat: parallelize unitig extraction and FASTA output d202ead385

Replace the non-atomic `set_visited` with atomic `fetch_or` bitmask operations to enable thread-safe node claiming. Introduce a two-phase extraction pipeline where `par_for_each_chain_unitig` builds chains in parallel and `for_each_remaining_unitig` sequentially handles residual cycles and junctions. Add `is_start` and `collect_from_start` to explicitly define unitig boundaries. Wrap `BufWriter` in a `Mutex` and use an `AtomicUsize` counter to ensure thread-safe concurrent FASTA output, refactoring the write logic into a shared closure for safe multi-threaded execution.

coissac merged commit ea2c594c86 into main

2026-06-05 08:41:08 +00:00

coissac deleted branch push-ruqusmkoyvwm

2026-06-05 08:41:08 +00:00

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Reference: OBIKmers/obikmer#16