feat: STARlong binary + long-read window-coverage filter#116
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BenjaminDEMAILLE wants to merge 3 commits into
Open
feat: STARlong binary + long-read window-coverage filter#116BenjaminDEMAILLE wants to merge 3 commits into
BenjaminDEMAILLE wants to merge 3 commits into
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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>
Add rustar-aligner-long binary (STAR's STARlong: identical CLI, forces the chaining-DP long-read stitcher via Parameters::long_read, matching how native STAR selects it by binary rather than a flag). Wire params.long_read through stitch_seeds_with_jdb_debug into a new window_read_coverage (ReadAlign_stitchPieces.cpp's WC accumulation, faithful to upstream's rLast=0 under-count for a seed starting at read position 0) and gate the winReadCoverageRelativeMin/winReadCoverageBasesMin cluster filter on long_read, since standard STAR does not filter clusters by seed coverage. Refactor stitch_seeds_core's preamble into prepare_stitch_input, shared with the (upcoming) STARlong chaining-DP stitcher stitch_seeds_long_read. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
rustar-aligner-longbinary (STAR's STARlong: identical CLI, forces the chaining-DP long-read stitcher viaParameters::long_read, matching how native STAR selects it by binary rather than a flag).params.long_readthroughstitch_seeds_with_jdb_debuginto a newwindow_read_coverage(ReadAlign_stitchPieces.cpp's WC accumulation, faithful to upstream'srLast=0under-count for a seed starting at read position 0) and gate thewinReadCoverageRelativeMin/winReadCoverageBasesMincluster filter onlong_read, since standard STAR does not filter clusters by seed coverage.docs-old/dev/porting-from-star-rs.md.Test plan