Push rxrxptuxltlp #12

2026-05-30T14:03:03Z

coissac commented

2026-05-30 14:03:03 +00:00

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coissac added 2 commits 2026-05-30 14:03:04 +00:00

refactor: aggregate query results at sequence level 708b0abf9b

Refactor the query pipeline to buffer partition outputs into a per-sequence `seq_results` vector, deferring final accumulation until all partitions complete. This ensures global position ordering before computing k-mer presence, counts, and coverage statistics. Additionally, removes a resolved TODO and documents a known BLAST false-positive issue where chloroplast and bacterial contaminants yield unrealistic high-confidence matches.

docs: clarify query pipeline, Findere trick, and input formats 8a0b898b4b

Fix a stray prefix in the README heading and update documentation to reflect the query pipeline's operation on `s-mers` (`s = k - z + 1`) with post-partition z-window filtering. Clarify the Findere trick, including k-mer size reduction, consecutive match requirements, and false positive rate calculations. Additionally, expand input format documentation to cover supported file extensions, gzip compression, recursive directory handling, and `query` command specifications.

coissac merged commit 728476a0a6 into main

2026-05-30 14:03:13 +00:00

coissac deleted branch push-rxrxptuxltlp

2026-05-30 14:03:13 +00:00

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Reference: OBIKmers/obikmer#12