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Refactor SSHash indexing to unify parsing modalities and optimize performance
- #93
#93
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Aug 29, 2026
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Refactor SSHash indexing to unify parsing modalities and optimize performance
#93
jermp
merged 14 commits into
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streaming-optimization
jermp/sshash:streaming-optimization
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Commits on Jul 25, 2026
one indexing modality: canonical minimizer at non-canonical density
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minor
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minor
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Commits on Aug 10, 2026
reverse-complement the kmer once, not every m-mer
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drop the incremental reverse-complement slide from minimizer_iterator
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Commits on Aug 18, 2026
centre-closest tie-break (Proposition 24): the scheme is now forward
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Commits on Aug 19, 2026
drop num_super_kmers: one tuple per minimizer position, checked at merge
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Commits on Aug 20, 2026
scripts: drop the regular/canonical distinction
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Commits on Aug 28, 2026
fix reverse buffer refill for kmer types wider than 64 bits
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streaming queries: same-minimizer memo for negative-in-positive streams
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Commits on Aug 29, 2026
rename the seed shortcut counters
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collapse the unreleased version bumps: current index version is 6.0.0
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print_table.py: one table for both k, with a markdown option
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added new run logs and updated table with results
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