Push ylnwstyzqwrt #22

2026-06-12T10:09:58Z

coissac commented

2026-06-12 10:09:58 +00:00

No description provided.

coissac added 2 commits 2026-06-12 10:09:59 +00:00

feat: add parallel k-mer counting and stats CLI f44fe042bc

Introduces allocation-free `sum()` and `count_nonzero()` methods for compact integer vectors, extending the `ColumnWeights` trait with `partial_kmer_counts`. Adds parallel partition scanning to the k-mer index for computing per-genome distinct k-mer counts, and exposes a new `--stats` CLI flag to output these statistics as CSV.

feat: add memory-aware parallel merge scheduling and CLI flags b5e027f23b

Introduces a memory-aware scheduling strategy for parallel partition merging that replaces unbounded concurrency with a First-Fit Decreasing approach gated by a thread-safe `MemoryBudget` semaphore. An adaptive expansion factor, seeded by a sequential pilot run, dynamically caps concurrent workers to prevent hashbrown OOMs. Adds a `--budget-fraction` CLI flag to configure RAM allocation, enhances the CLI to accept multiple indexes, and introduces comprehensive partition diagnostics including memory utilization tracking, concurrency metrics, and statistical summaries with ASCII histograms. Updates documentation and navigation accordingly.

coissac merged commit 97e3fb9761 into main

2026-06-12 10:10:04 +00:00

coissac deleted branch push-ylnwstyzqwrt

2026-06-12 10:10:04 +00:00

Sign in to join this conversation.

1 Participants

Notifications

Due Date

No due date set.

Dependencies

No dependencies set.

Reference: OBIKmers/obikmer#22