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V4 streaming primary - #304

Merged

MrOlm merged 15 commits into

masterfrom

v4-streaming-primary

Jul 16, 2026

Merged

V4 streaming primary#304
MrOlm merged 15 commits into
masterfrom
v4-streaming-primary

Commits on Jul 14, 2026
- Streaming union-find primary clustering + sparse skani
  
  MrOlm
  and
  claude
  committed
  9ef5e11
- Fix skani alignment coverage being a percent, not a fraction
  
  MrOlm
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  claude
  committed
  f50c790
- Add pyskani backend: sketch each genome once, compare in-process
  
  MrOlm
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  claude
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  62299da
- Pass --min-af 0 to sparse skani primary clustering
  
  MrOlm
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  claude
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  6e56349
- Keep skani's aligned-fraction filter for primary clustering
  
  MrOlm
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  claude
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  30ef829
- Don't let estimate_time kill a run on an unknown S_algorithm
  
  MrOlm
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  claude
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  5ed4d6a
- One-pass skani: reuse primary's comparisons for secondary clustering
  
  MrOlm
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  71e2328
- Make skani the default; remove pyskani and --low_ram_primary_clustering
  
  MrOlm
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  claude
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  783821d
Commits on Jul 15, 2026
- Fix ScaffoldLevel_dRep.py crashing on MUMmer 3
  
  MrOlm
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  claude
  committed
  626db0c
- Add v4.0.0 release notes
  
  MrOlm
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  claude
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  1650d07
- Drop unused progress arg from load_skani_sparse_edges
  
  MrOlm
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  claude
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  034fb18
- Cycle a small palette for cluster colors instead of one shade each
  
  MrOlm
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  bb51af7
- Release 4.0.0
  
  MrOlm
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  claude
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  569c311
Commits on Jul 16, 2026
- update readme
  MrOlm
  committed
  b888eb4
- Revise dRep v4 section in README
  MrOlm
  authored
  9eebddd

Commits

Commits on Jul 14, 2026

Commits on Jul 15, 2026

Commits on Jul 16, 2026