Phase 14: STARsolo single-cell support (MVP + CellRanger matching)

[iandriver]

What & why

Implements STARsolo Phases 14.1–14.4 (the 10x Chromium Gene-count MVP) plus the
CellRanger 4.x/5.x-matching flag set, ported faithfully from STAR's source and
verified byte-identical against real STARsolo (3/3 deterministic) via a
Linux-container differential harness.

Changes

• src/solo/ (new):
  • mod.rs — --soloType/params plumbing, barcode-read input (SoloReadReader),
    SoloContext, per-read processing, CellRanger4 adapter clip
  • whitelist.rs — 2-bit barcode packing, sorted-whitelist load, read-stage CB
    matching (exact/1MM/1MM_multi) + UMI checks (STAR SoloReadBarcode_getCBandUMI.cpp)
  • gene.rs — per-read gene assignment (--soloStrand), reuses quant::overlapping_genes
  • count.rs — UMI dedup (Exact/NoDedup/1MM_All/1MM_Directional/1MM_CR),
    MultiGeneUMI(_CR) filtering, 1MM_multi_Nbase_pseudocounts CB posterior,
    raw matrix.mtx/barcodes.tsv/features.tsv writer
• src/lib.rs: new align_reads_solo loop (reads cDNA + barcode in lockstep,
  aligns cDNA, quantifies per cell); src/params/mod.rs: --solo* params + validation
• CellRanger-matching flags: --clipAdapterType CellRanger4,
  --outFilterScoreMin, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts,
  --soloUMIfiltering MultiGeneUMI_CR, --soloUMIdedup 1MM_CR
• Tests / harnesses: tests/alignment_features.rs
  (+test_starsolo_gene_matrix, +test_starsolo_cellranger_style_matrix),
  test/solo_cellranger_diff.py + Dockerfile.solodiff + solo_diff_docker.sh
  (live STAR diff), test/solo_bench.py + Dockerfile.bench
  (CellRanger vs STARsolo vs rustar runtime/stats benchmark scaffold)

Notes for reviewers

• 479 lib + 11 integration tests, 0 clippy warnings, cargo fmt clean.
• The live STAR diff runs in a Linux container because STAR 2.7.11b reads 0 reads
  on Apple-Silicon macOS (a known STAR/macOS bug).
• Design notes and sub-phase tracking in docs-old/phase14_starsolo.md + ROADMAP.md.
• The 1MM_multi posterior cbMinP threshold and 1MM_Directional greedy variant
  are documented as approximations to revisit (default 1MM_All path is exact).

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