docs: STAR-rs porting groundwork (attribution + conventions) - #106
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CI's clippy advanced to 1.97 (new lints fail the `-D warnings` gate) and rustsec flagged several advisories in the dependency tree. Both block all PRs. Clippy: - src/index/suffix_array.rs: assert!(x == 0) -> assert_eq! (manual_assert_eq) - src/io/sam.rs, tests/alignment_features.rs: byte-slice literals -> byte strings, e.g. [b'S', b'M'] -> *b"SM" (byte_char_slices) - src/quant/transcriptome.rs: if-let/else-return-None -> `?` (question_mark) Security audit (Cargo.lock only, no manifest change): - memmap2 0.9.10 -> 0.9.11 (RUSTSEC-2026-0186, out-of-bounds pointer offset) - crossbeam-epoch 0.9.18 -> 0.9.20 (RUSTSEC-2026-0204, invalid pointer deref) - anyhow 1.0.102 -> 1.0.104 (RUSTSEC-2026-0190, unsound downcast_mut) No behavioural change. Unblocks CI for open and future PRs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Add LICENSES/STAR_RS_LICENSE (STAR-rs MIT notice, Copyright (c) 2026 Benjamin Demaille) and note it in LICENSES/README.md, for attribution of modules ported from STAR-rs. STAR-rs is dual MIT-OR-Apache; ported code is taken under its MIT option, compatible with this repo's MIT license. Add docs-old/dev/porting-from-star-rs.md documenting the STAR-rs to rustar-aligner type/module mapping, the licensing and cellranger reference-only caveat, the determinism decision (adopt STAR-rs's thread-invariant, no-rand model), and how to validate ports against native STAR via the existing test/ harness with DIVERGENCES.md as the acceptance spec. This is the base of a series of themed, dependency-stacked PRs bringing the STAR-rs feature surface (WASP, clipping, signal tracks, genome transforms, STARlong, STARsolo, ...) into rustar-aligner. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What
Groundwork for a series of themed, dependency-stacked PRs bringing the STAR-rs feature surface into rustar-aligner. This first PR adds no code paths, only attribution and conventions:
LICENSES/STAR_RS_LICENSE+ a note inLICENSES/README.md— the STAR-rs MIT notice (© 2026 Benjamin Demaille), for attribution of modules ported from STAR-rs. STAR-rs is dualMIT OR Apache-2.0; ported code is taken under its MIT option, compatible with this repo's MIT license.docs-old/dev/porting-from-star-rs.md— the STAR-rs → rustar-aligner type/module mapping, the cellranger reference-only caveat, the determinism decision (adopt STAR-rs's thread-invariant, no-randmodel; flagged for discussion), and how to validate ports against native STAR using the existingtest/harness with STAR-rs'sDIVERGENCES.mdas the acceptance spec.Why
STAR-rs is a clean-room Rust re-port of STAR 2.7.11b, validated byte-identical vs native STAR. rustar-aligner already covers SE/PE alignment, splice junctions, two-pass, chimeric, GeneCounts, TranscriptomeSAM and sorted BAM; STAR-rs additionally has STARsolo, STARlong, WASP, genome transforms, signal tracks, clipping, peOverlap, SuperTranscriptome, liftOver and more. This PR is the base of the stack that brings those over one theme at a time.
Next in the stack
vW/vA/vG,--varVCFfile,--waspOutputMode) — stacks on this PR.Notes
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