Push rwqsmuvystym #24

2026-06-12T19:33:16Z

coissac commented

2026-06-12 19:33:16 +00:00

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coissac added 3 commits 2026-06-12 19:33:16 +00:00

feat: dynamically compute seed expansion based on RSS 2bc189e962

Introduce a `peak_rss_bytes()` utility for accurate per-phase RAM measurement. Replace the genome-length heuristic with a dynamic seed expansion ratio based on actual RSS delta. Explicitly drop the `GraphDeBruijn` instance before MPHF construction to prevent resource contention and ensure proper memory management.

refactor: parallelize merge and partition logic with obipipeline ba49af6f9e

Introduce the `obipipeline` dependency and refactor merge and partition logic to leverage parallel execution. Update `merge_partitions` to use rayon with dynamic memory budgeting and concurrency control via a pilot run. Refactor Pass 1 to concurrently read unitigs, filter kmers through a shared `LayeredMap`, and populate the graph safely. Simplify diagnostics to report total kmer counts and replace manual flags with graph length validation.

refactor: parallelize merge layer with WorkerPool pipeline b2c8373586

Replaces the synchronous sequential loop with a multi-threaded pipeline using `WorkerPool` and custom stage macros. Shared mutable state is wrapped in `Arc<Mutex<>>` for thread-safe updates, while pipeline errors are centralized via `Arc<Mutex<Option<String>>>` to propagate failures before thread join.

coissac merged commit 9ea1dff5d6 into main

2026-06-12 19:33:21 +00:00

coissac deleted branch push-rwqsmuvystym

2026-06-12 19:33:21 +00:00

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Reference: OBIKmers/obikmer#24