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Remove dead code; stdout writers are the file writers on another output - #365

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BenjaminDEMAILLE wants to merge 17 commits into

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chore/dead-code

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Remove dead code; stdout writers are the file writers on another output#365
BenjaminDEMAILLE wants to merge 17 commits into
mainfrom
chore/dead-code

Commits on Oct 29, 2026
- nM: STAR's accumulated mismatch count, not a recount
  
  BenjaminDEMAILLE
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  460ddba
- Write the forward-strand mate of a pair first
  
  BenjaminDEMAILLE
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  040b847
- Drop the mate-2 exon-subset dedup of finalized pairs
  
  BenjaminDEMAILLE
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  b00182f
- Drop the read when a window full of anchors receives another align
  
  BenjaminDEMAILLE
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  c94e6c3
- STARsolo: STAR's EM for --soloMultiMappers, zeros written
  
  BenjaminDEMAILLE
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  d8322e5
- STARsolo: keep gene-ambiguous reads with a 1MM_multi barcode
  
  BenjaminDEMAILLE
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  824cc3f
- STARsolo: --soloUMIfiltering for the SJ feature
  
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  1fd99a3
- Docs: the DIVERGENCE.md 5 residuals are fixed
  
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  0144a96
- Splice-junction database: FxHashMap instead of SipHash
  
  BenjaminDEMAILLE
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  7e2212c
- Stitcher: store a recorded transcript's window score and mapped length
  
  BenjaminDEMAILLE
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  73f7afe
- Junction scan: stop once no later position can win
  
  BenjaminDEMAILLE
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  457c34c
- Stitcher: memoize flank extensions in large windows
  
  BenjaminDEMAILLE
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  45aa4c9
- Transcript dedup: compare CIGARs without building strings
  
  BenjaminDEMAILLE
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  c44c54b
- Stitcher: backtrack on one transcript instead of cloning at each branch
  
  BenjaminDEMAILLE
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  a29228f
- Junction scan: fetch the scan's bases in bulk
  
  BenjaminDEMAILLE
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  e7853ec
Commits on Oct 30, 2026
- Stitcher: keep the window memo tables between windows
  
  BenjaminDEMAILLE
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  claude
  committed
  aeba641
Commits on Nov 2, 2026
- Remove dead code; stdout writers are the file writers on another output
  
  BenjaminDEMAILLE
  and
  claude
  committed
  bcddd31

Commits

Commits on Oct 29, 2026

Commits on Oct 30, 2026

Commits on Nov 2, 2026