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Integration/pr batch 1 - #77

Merged

Psy-Fer merged 57 commits into

mainfrom

integration/pr-batch-1

May 29, 2026

Merged

Integration/pr batch 1#77
Psy-Fer merged 57 commits into
mainfrom
integration/pr-batch-1

Commits on May 12, 2026
- feat(params): accept --limitGenomeGenerateRAM for STAR CLI compatibility
  pinin4fjords
  committed
  b8ba281
- fix(chimeric): create output parent directory before writing
  pinin4fjords
  committed
  8589859
- fix(bam): subtract Phred+33 offset from QUAL before writing to BAM
  pinin4fjords
  committed
  b501420
- fix(transcriptome-bam): write per-record RG:Z: tag matching @RG header
  pinin4fjords
  committed
  27e3da1
- feat(bam): populate @PG header with PN/VN/CL fields
  pinin4fjords
  committed
  ed59a6c
- chore(params): trim verbose doc comment
  pinin4fjords
  committed
  9a7be3e
- chore(chimeric): remove narrative test comment
  pinin4fjords
  committed
  176a94c
- chore(bam): remove narrative inline comment
  pinin4fjords
  committed
  586f206
- chore(transcriptome-bam): remove narrative comments
  pinin4fjords
  committed
  5930c04
- chore(bam): remove narrative comments
  pinin4fjords
  committed
  0e49edd
- fix(transcriptome-bam): populate mate fields on paired-end records
  pinin4fjords
  committed
  8ffaddd
- fix(bam): emit SAM-spec NM:i: tag distinct from STAR-internal nM:i:
  pinin4fjords
  committed
  aa05ad0
- feat(bam): emit XS:A: strand tag when --outSAMstrandField intronMotif
  pinin4fjords
  committed
  d4a382b
- feat(output): emit Log.out, Log.progress.out, _STARpass1/SJ.out.tab
  
  pinin4fjords
  and
  claude
  committed
  1a55cae
- fix(sjdb): key SpliceJunctionDb in genome-absolute 0-based coordinates
  
  pinin4fjords
  and
  claude
  committed
  6724959
- revert(stats): drop Log.out / Log.progress.out stub writers
  
  pinin4fjords
  and
  claude
  committed
  e91433a
- chore(params): warn at runtime when --limitGenomeGenerateRAM is set
  
  pinin4fjords
  and
  claude
  committed
  cc3e48a
- fix(sjdb): off-by-one on stitch-time acceptor coordinate
  
  pinin4fjords
  and
  claude
  committed
  ac09650
- fix: decode Gsj-region SA hits into split splice seeds
  
  pinin4fjords
  and
  claude
  committed
  abf856e
- fix(stitch): use sjdb_score in place of motif_score on annotated junctions
  
  pinin4fjords
  and
  claude
  committed
  e09748b
- fix(score): score_annotated_junction helper uses replacement not addition
  
  pinin4fjords
  and
  claude
  committed
  6165b22
- fix(stats): route reads exceeding --outFilterMultimapNmax to too_many_loci
  
  pinin4fjords
  and
  claude
  committed
  0ab80c5
- refactor(stats): drop redundant n_for_mapq conditional in PE caller
  
  pinin4fjords
  and
  claude
  committed
  3f0377e
Commits on May 16, 2026
- Merge branch 'main' into pr/pinin4fjords/51
  flying-sheep
  committed
  4784bd0
- Merge branch 'main' into pr/pinin4fjords/45
  flying-sheep
  committed
  0ab761f
- Merge branch 'main' into pr/pinin4fjords/42
  flying-sheep
  committed
  aaa44de
- Merge branch 'main' into pr/pinin4fjords/41
  flying-sheep
  committed
  94f7e78
- Merge branch 'main' into pr/pinin4fjords/37
  flying-sheep
  committed
  c2967b0
- Merge branch 'main' into fix/chim-parent-dir-create
  flying-sheep
  authored
  3fa407e
- Merge branch 'main' into pr/pinin4fjords/41
  flying-sheep
  committed
  4bb2803
- Merge branch 'main' into pr/pinin4fjords/43
  flying-sheep
  committed
  ee0bfee
- Merge branch 'main' into pr/pinin4fjords/44
  flying-sheep
  committed
  e5e7790
- fix test
  flying-sheep
  committed
  2b206d1
Commits on May 17, 2026
- Merge branch 'main' into pr/pinin4fjords/36
  flying-sheep
  committed
  8ef5e57
- Merge branch 'main' into fix/pg-header-content
  flying-sheep
  committed
  7134337
- Merge branch 'main' into fix/xs-strand-tag
  flying-sheep
  committed
  5c08c3c
- upstream changes
  flying-sheep
  committed
  a729801
- chore: switch sam attributes to bitflags
  flying-sheep
  committed
  d177215
Commits on May 29, 2026

Commits

Commits on May 12, 2026

Commits on May 16, 2026

Commits on May 17, 2026

Commits on May 29, 2026