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feat(quant): unspliced targets in TranscriptomeSAM, splicing-status tag and GeneSplicing counts for bulk total RNA-seq - #283

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feature/unspliced-bulk-quant

Commits on Oct 8, 2026
- feat(quant): port STAR's Velocyto transcript-model classifier for bulk reads
  
  BenjaminDEMAILLE
  and
  claude
  committed
  afca227
- feat(quant): --quantMode GeneVelocyto, bulk spliced/unspliced/ambiguous gene table
  
  BenjaminDEMAILLE
  and
  claude
  committed
  0269072
- feat(quant): --quantTranscriptomePreMRNA BanRetainedIntron for TranscriptomeSAM
  
  BenjaminDEMAILLE
  and
  claude
  committed
  e266ba9
- test: new bulk options leave existing outputs unchanged
  
  BenjaminDEMAILLE
  and
  claude
  committed
  10537d7
- test: simulated total RNA mixture for GeneVelocyto and BanRetainedIntron
  
  BenjaminDEMAILLE
  and
  claude
  committed
  80f0d93
- docs: bulk total RNA-seq guide, DIVERGENCE 1.4 and CHANGELOG entry
  
  BenjaminDEMAILLE
  and
  claude
  committed
  937bac8
- refactor(quant): rename GeneVelocyto to GeneSplicing
  
  BenjaminDEMAILLE
  and
  claude
  committed
  bc68f09
- feat(quant): unspliced <gene_id>-I targets in TranscriptomeSAM
  
  BenjaminDEMAILLE
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  claude
  committed
  d87ed7d
- test: unspliced targets in the bulk integration tests
  
  BenjaminDEMAILLE
  and
  claude
  committed
  657464b
- refactor(quant): remove --quantTranscriptomePreMRNA BanRetainedIntron
  
  BenjaminDEMAILLE
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  claude
  committed
  80c54a0
- feat(sam): opt-in sp:A splicing-status tag in the genomic SAM/BAM
  
  BenjaminDEMAILLE
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  claude
  committed
  6952271
- docs: bulk total RNA guide for unspliced targets, sp tag and GeneSplicing
  
  BenjaminDEMAILLE
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  claude
  committed
  4583556
- bench: public whole-blood total RNA benchmark for unspliced targets
  
  BenjaminDEMAILLE
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  claude
  committed
  7bcdc3a
- fix: build and lint on rebased main
  
  BenjaminDEMAILLE
  and
  claude
  committed
  60cf4bf
- refactor(params): own flags for GeneSplicing and the sp tag
  
  BenjaminDEMAILLE
  and
  claude
  committed
  c03413c

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feat(quant): unspliced targets in TranscriptomeSAM, splicing-status tag and GeneSplicing counts for bulk total RNA-seq - #283

feat(quant): unspliced targets in TranscriptomeSAM, splicing-status tag and GeneSplicing counts for bulk total RNA-seq#283
BenjaminDEMAILLE wants to merge 15 commits into
mainfrom
feature/unspliced-bulk-quant

Commits on Oct 8, 2026

feat(quant): port STAR's Velocyto transcript-model classifier for bulk reads

feat(quant): --quantMode GeneVelocyto, bulk spliced/unspliced/ambiguous gene table

feat(quant): --quantTranscriptomePreMRNA BanRetainedIntron for TranscriptomeSAM

test: new bulk options leave existing outputs unchanged

test: simulated total RNA mixture for GeneVelocyto and BanRetainedIntron

docs: bulk total RNA-seq guide, DIVERGENCE 1.4 and CHANGELOG entry

refactor(quant): rename GeneVelocyto to GeneSplicing

feat(quant): unspliced <gene_id>-I targets in TranscriptomeSAM

test: unspliced targets in the bulk integration tests

refactor(quant): remove --quantTranscriptomePreMRNA BanRetainedIntron

feat(sam): opt-in sp:A splicing-status tag in the genomic SAM/BAM

docs: bulk total RNA guide for unspliced targets, sp tag and GeneSplicing

bench: public whole-blood total RNA benchmark for unspliced targets

fix: build and lint on rebased main

refactor(params): own flags for GeneSplicing and the sp tag