V4 streaming primary - #304

Merged

MrOlm merged 15 commits into

v4-streaming-primary

Jul 16, 2026

Commits on Jul 14, 2026

Streaming union-find primary clustering + sparse skani

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Fix skani alignment coverage being a percent, not a fraction

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Add pyskani backend: sketch each genome once, compare in-process

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Pass --min-af 0 to sparse skani primary clustering

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Keep skani's aligned-fraction filter for primary clustering

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Don't let estimate_time kill a run on an unknown S_algorithm

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One-pass skani: reuse primary's comparisons for secondary clustering

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Make skani the default; remove pyskani and --low_ram_primary_clustering

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Commits on Jul 15, 2026

Commits on Jul 16, 2026