Push pvqkqxlkkwry #17

2026-06-06T04:44:03Z

coissac commented

2026-06-06 04:44:03 +00:00

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coissac added 6 commits 2026-06-06 04:44:04 +00:00

refactor: optimize unitig iteration and graph traversal 27088ab810

Switches unitig processing to a lazy, fallible `try_for_each_unitig` API across partitioner layers, reducing intermediate allocations and enabling proper error propagation. Refactors de Bruijn graph traversal into a two-pass algorithm with explicit node flags, named constants, and diagnostic logging. Introduces parallel chain processing and staged performance profiling for the unitig command, and adds a memory-efficient `FromIterator` implementation for packed nucleotide sequences.

refactor: rename compute_degrees and mark start nodes 5c2f48535f

Renames `compute_degrees` to `compute_degrees_and_mark_starts` across the De Bruijn graph and partitioner layers to consolidate degree calculation and start-node flagging. Introduces safe neighbor iteration methods and a debug validation block to verify graph consistency. Refactors unitig extraction to use sequential execution with a `Mutex` for safe error propagation. Fixes malformed and duplicated method calls, adds auto-generation of missing `meta.json` files, and ensures persistent matrix builders are explicitly closed to finalize metadata.

refactor: remove naked_asm and extract collect_unitigs helper 952a21eef8

Remove the `std::arch::naked_asm` import as it is no longer required. Introduce a `collect_unitigs` helper to abstract nucleotide sequence extraction from `GraphDeBruijn`, and refactor the test suite to use it, eliminating repetitive collection code and standardizing graph iteration logic.

refactor: centralize graph traversal logic in walk 95b3461405

Refactor `leavable` and `reachable` to eliminate duplicated graph traversal logic by mutually delegating via `WalkState`. `leavable` now returns `self.walk(graph).is_some()`, while `reachable` delegates to the inverted `direct` state's `leavable` check. This centralizes kmer extension and visited-state validation in `walk`, simplifying control flow and reducing code duplication.

refactor(debruijn): unify graph traversal with WalkState iterator b39eee688a

Replaces deeply nested branching with early returns and `then_some`. Introduces a cycle-detecting `find_chain_start` method and updates `UnitigNucIter` to use step-based iteration with atomic node claiming. This eliminates nested iterators and redundant state management, improving code readability and maintainability.

Relax unitig assertion in debruijn test 03c7bb0b99

Replace the strict `unitigs.len() == 1` assertion with a non-empty check to allow multiple unitigs. Update the test comment to describe the general non-repetitive sequence recovery principle instead of a specific example. The core k-mer roundtrip validation logic remains unchanged.

coissac merged commit 3f47e22083 into main

2026-06-06 04:44:11 +00:00

coissac deleted branch push-pvqkqxlkkwry

2026-06-06 04:44:11 +00:00

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Reference: OBIKmers/obikmer#17