Integration/pr batch 1#77

Merged

Psy-Fer merged 57 commits into

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integration/pr-batch-1

May 29, 2026

Commits on May 12, 2026

feat(params): accept --limitGenomeGenerateRAM for STAR CLI compatibility
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fix(chimeric): create output parent directory before writing
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fix(bam): subtract Phred+33 offset from QUAL before writing to BAM
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fix(transcriptome-bam): write per-record RG:Z: tag matching @RG header
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feat(bam): populate @PG header with PN/VN/CL fields
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chore(params): trim verbose doc comment
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chore(chimeric): remove narrative test comment
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chore(bam): remove narrative inline comment
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chore(transcriptome-bam): remove narrative comments
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chore(bam): remove narrative comments
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fix(transcriptome-bam): populate mate fields on paired-end records
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fix(bam): emit SAM-spec NM:i: tag distinct from STAR-internal nM:i:
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feat(bam): emit XS:A: strand tag when --outSAMstrandField intronMotif
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feat(output): emit Log.out, Log.progress.out, _STARpass1/SJ.out.tab

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fix(sjdb): key SpliceJunctionDb in genome-absolute 0-based coordinates

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revert(stats): drop Log.out / Log.progress.out stub writers

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chore(params): warn at runtime when --limitGenomeGenerateRAM is set

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fix(sjdb): off-by-one on stitch-time acceptor coordinate

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fix: decode Gsj-region SA hits into split splice seeds

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fix(stitch): use sjdb_score in place of motif_score on annotated junctions

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fix(score): score_annotated_junction helper uses replacement not addition

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fix(stats): route reads exceeding --outFilterMultimapNmax to too_many_loci

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refactor(stats): drop redundant n_for_mapq conditional in PE caller

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Commits on May 16, 2026

Commits on May 29, 2026