Eric Coissac b0890d1781 Add sparse storage variant to PersistentCompactIntMatrix ...

Introduce a new `Sparse` format alongside existing `Columnar` and `Packed` variants, enabling optimized row-major pairwise counting for distance and similarity metrics via the `CountPartials` trait. Update storage detection priorities, extend matrix dispatch logic to sparse backends, and correct diagonal/off-diagonal formulas in bit matrix partial computations. Expand layer APIs with format-agnostic `nonzero_iter`, update usage documentation for the `--sparse` flag, and add comprehensive tests verifying roundtrip integrity and metric equivalence against dense implementations.

2026-08-28 19:06:39 +02:00

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annotate.md

docs: add obikmer user guide and MkDocs build configuration

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dump.md

docs: add obikmer user guide and MkDocs build configuration

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estimate.md

docs: add obikmer user guide and MkDocs build configuration

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filter.md

docs: add obikmer user guide and MkDocs build configuration

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index_command.md

docs: add obikmer user guide and MkDocs build configuration

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merge.md

docs: add obikmer user guide and MkDocs build configuration

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name-tree.md

add name-tree command and fix --free-loss cost matrix

2026-08-16 13:11:06 +02:00

pack.md

Add sparse storage variant to PersistentCompactIntMatrix

2026-08-28 19:06:39 +02:00

phylo.md

feat(phylo): add --iqtree-min-freq to filter rare nucleotide states

2026-08-17 11:06:03 +02:00

predicates.md

docs: add obikmer user guide and MkDocs build configuration

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query.md

docs: add obikmer user guide and MkDocs build configuration

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reindex.md

docs: add obikmer user guide and MkDocs build configuration

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select.md

docs: add obikmer user guide and MkDocs build configuration

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superkmer.md

docs: add obikmer user guide and MkDocs build configuration

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unitig.md

docs: add obikmer user guide and MkDocs build configuration

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utils.md

docs: add obikmer user guide and MkDocs build configuration

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