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feat: add `--quantMode TranscriptomeSAM` output - #7

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ewels:feat/transcriptome-sam

Commits on Apr 17, 2026
- feat: add --runRNGseed and seeded primary tie-break
  
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- Add --outSAMattrRGline flag and emit @RG header + RG:Z tags
  
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- chore(simplify): use SliceRandom::shuffle for tied-prefix shuffle
  
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- chore(simplify): tighten tie-shuffle comments
  
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- chore(simplify): use std::hash::DefaultHasher directly
  
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- chore(simplify): replace where-clause with impl Fn on shuffle_tied_prefix
  
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- chore(simplify): drop dead rg_ids() call and redundant attrs gate
  
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- chore(simplify): introduce primary_rg_id helper for writer callsites
  
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- chore(simplify): rewrite parsed_rg_lines with Vec::split
  
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- chore: remove dead SamWriter::write_unmapped
  
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- chore: apply cargo fmt
  
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- chore: apply cargo fmt
  
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Commits on Apr 20, 2026
- Merge branch 'main' into feat/run-rng-seed
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- Merge pull request #5 from ewels/feat/run-rng-seed
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- Merge branch 'main' into feat/sam-rg-line
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- Fix merge conflict squashing } braket
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- Merge pull request #6 from ewels/feat/sam-rg-line
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  0763745
Commits on Apr 21, 2026
- feat(quant): add TranscriptomeIndex built from GTF exon groups
  
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- feat(quant): project genome alignments onto transcripts (align_to_transcripts)
  
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- feat(quant): filter modes + softclip extension for transcriptome SAM
  
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- feat(params): --quantTranscriptomeSAMoutput + TranscriptomeSAM validation
  
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- feat(io/bam,lib): wire Aligned.toTranscriptome.out.bam pipeline
  
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- test: integration test for --quantMode TranscriptomeSAM
  
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- chore(simplify): drop dead Display + allow_single_end on QuantTranscriptomeSAMoutput
  
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- chore(simplify): share a single rc_encode helper in transcriptome builders
  
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- chore(simplify): emit PE transcriptome records with one build call per mate
  
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- chore(simplify): share primary-hit + MAPQ picker between SE and PE
  
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- chore(simplify): share BGZF writer setup between BamWriter constructors
  
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- chore(simplify): collapse locals in extend_softclips trailing fixup
  
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- chore(simplify): tighten filter_and_project docs + drop unread read_seq clone
  
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- chore(simplify): fix stale mate_or_junction_before comment in align_to_one_transcript
  
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- chore(simplify): drop speculative BamWriter::header accessor
  
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- chore(simplify): accept IntoIterator in build_transcriptome_records_pe
  
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- chore(simplify): drop redundant StdHashMap alias in transcriptome tests
  
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- chore: apply cargo fmt
  
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Commits on Apr 22, 2026
- feat(quant): add tr_exi cumulative exon offset to TranscriptomeIndex
  
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- feat(quant): add gene interning (gene_ids/names/biotypes + tr_gene_idx)
  
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- fix(quant): compute tr_exi in STAR's sorted order, not insertion order
  
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- feat(quant): write transcriptInfo.tab in STAR's exact byte format
  
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- feat(quant): write exonInfo.tab in STAR's exact byte format
  
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- feat(quant): write geneInfo.tab in STAR's exact byte format
  
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- feat(quant): write exonGeTrInfo.tab in STAR's exact byte format
  
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- feat(quant): write sjdbList.fromGTF.out.tab in STAR's exact byte format
  
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- feat(quant): load TranscriptomeIndex from on-disk STAR files
  
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- feat: persist transcriptome index at genomeGenerate, load at alignReads
  
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- feat(align): add i_frag mate index to Exon
  
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- feat(quant): handle mate boundary in transcriptome projection
  
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- feat(align): add PairedAlignment::combined_transcript_for_projection
  
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- test: verify byte-format parity of all 5 STAR-compatible index files
  
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- fix(quant): match STAR's geneInfo.tab fallback strings
  
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- test: add diff_star_transcriptome.sh — byte-for-byte parity script
  
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- fix(genome): match STAR's genomeParameters.txt byte-for-byte
  
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- chore(simplify): reuse Genome::position_to_chr in TranscriptomeIndex loader
  
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- chore(simplify): lift GTF attribute names + MissingGeneType to constants
  
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- test: simplify diff script with a symlink pointing to per-tool index dir
  
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- chore(simplify): drop redundant tr_gene_id string field from TranscriptomeIndex
  
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- fix(params): don't require --sjdbGTFfile at alignReads when the index has it
  
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- fix(io/bam): write header with a lenient validator (STAR tRNA names)
  
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- Merge upstream/dev into feat/transcriptome-sam
  
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- chore(simplify): collapse try_pair_transcripts now that all callers supply the combined score
  
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Commits

Commits on Apr 17, 2026

Commits on Apr 20, 2026

Commits on Apr 21, 2026

Commits on Apr 22, 2026