feat: WASP allele-specific-mapping filter (SE + PE) - #108
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BenjaminDEMAILLE wants to merge 7 commits into
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feat: WASP allele-specific-mapping filter (SE + PE)#108BenjaminDEMAILLE wants to merge 7 commits into
BenjaminDEMAILLE wants to merge 7 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>
Port STAR's WASP filter (--waspOutputMode SAMtag, --varVCFfile) from STAR-rs `crates/star-align/src/star_wasp.rs`. A uniquely-mapped read overlapping heterozygous SNVs is re-mapped with every alternative-allele combination; if all re-maps land on the identical locus it passes (vW:i:1), otherwise a failure code (2..7) is reported. Emits vW, and vA/vG when requested in --outSAMattributes. - src/wasp/mod.rs: load_vcf, wasp_type (re-map decision), wasp_variants (vG/vA), and record annotation. Works in base-code space; variant/read overlap is computed by walking the transcript CIGAR (same convention as build_md_tag), so it does not depend on the exon read-coordinate frame. - src/params: add --waspOutputMode (None|SAMtag) and --varVCFfile, validation (SAMtag requires a VCF), and vW/vA/vG in --outSAMattributes. - src/lib.rs: load the VCF once per run, re-map with a WASP-relaxed parameter set (match_nmin=0, multimap_score_range=1, multimap_nmax=10, matching STAR), and stamp vW/vA/vG onto the SAM records in the single-end path. Paired-end WASP is a follow-up. See docs-old/dev/porting-from-star-rs.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Replace the single giant phase-log paragraph and the stale hardcoded test count / known-issues list with a short faithfulness summary and a pointer to ROADMAP.md / CHANGELOG.md / docs-old for per-phase history. Refresh the source layout (params/ split, cpu.rs, sa_build.rs, sjdb_insert.rs, transcriptome.rs, log.rs) and the dependency list (caps-sa, mimalloc, rand 0.10, tempfile as a runtime dep) to match the current tree. Documentation only. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Complete the WASP filter for paired-end reads, the documented follow-up to the single-end port (3e84d97). Ports STAR-rs `wasp_type_pe` / `wasp_variants_pe` into rustar-aligner's two-transcript-per-pair model. - src/wasp/mod.rs: add wasp_variants_pe (combined vG/vA over mate1 then mate2, STAR's `mate1 ++ rc(mate2)` combined-transcript order), wasp_type_pe (single vW code: walk each mate's variants in its SAM frame, apply every allele combination, map back to forward mates, and re-map the pair via align_paired_read with the WASP-relaxed params; a combination passes only if exactly one both-mapped pair lands on the same exons for both mates), and annotate_records_pe (both mate records share vW/vA/vG; multimapped pairs overlapping variants get vW:i:2). - src/lib.rs: build the WaspContext once in align_reads_paired_end and stamp vW/vA/vG onto the built pair records, mirroring the single-end path. Gate green: cargo build, clippy -D warnings, fmt, 464 tests (2 new PE variant-frame unit tests). Byte-level validation against native STAR via the test/ harness is a separate step. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
--waspOutputMode SAMtag,--varVCFfile) for both single-end and paired-end reads.docs-old/dev/porting-from-star-rs.md— this PR is now WASP-only. Clipping, signal tracks, genome transforms, and STARlong now have their own PRs (see stack below).Stack
Test plan