Wasp consolidation - #137
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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>
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>
(matches STAR); wire into pipelined loop
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July 27, 2026 06:39
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WASP allele-specific-mapping filter (
--waspOutputMode SAMtag) — consolidated + STAR-faithful (closes #108)Consolidates BenjaminDEMAILLE's WASP PR, with the two review-flagged divergences from real STAR fixed and the feature validated byte-for-byte against STAR 2.7.11b.
WASP (van de Geijn et al. 2015) removes reference-mapping bias: a read overlapping a heterozygous SNV is re-mapped with the allele swapped; if it no longer maps to the same locus, it's flagged. rustar emits STAR's
vW(pass/fail code) plus opt-invA/vGtags.Closes #108.
Fixes vs the original port (verified against
ReadAlign_waspMap.cpp)1. Re-map used relaxed filters (STAR-rs quirk) → now uses the user's params unmodified.
The port's
wasp_remap_paramssetout_filter_match_nmin = 0,out_filter_match_nmin_over_lread = 0.0,out_filter_multimap_score_range = 1,out_filter_multimap_nmax = 10. STAR's WASP re-map iswaspRA = new ReadAlign(Pin,…)sharing the sameP, running the normalmapOneRead()→multMapSelect()→mappedFilter(); a swapped read failingmappedFilterunder the user's own thresholds becomeswaspType=4. Relaxing the filters lets swapped reads pass WASP that STAR would reject. Fixed:wasp_remap_paramsreturnsparams.clone()verbatim.2. Multimapper
vWsemantics were per-locus → now keyed off the primary alignment.STAR computes one
waspTypefromtrBest(the primary): if the primary overlaps ≥1 variant and the read multimaps →waspType=2stamped on all of the read's records; if the primary overlaps no variant → novWon any record (even if a secondary locus does). The port stampedvW:2per-record only where that record's own locus overlapped a variant. Fixed for both SE and PE (vA/vGstay per-record, matching STAR's per-alignmentvariationAdjust).Integration into the current pipeline
The PR was written against the old single-threaded loop; it's now wired into the pipelined SE + PE drivers — the VCF is loaded once per run into a shared read-only
WaspContext, andannotate_records_se/_perun per mapped read/pair in the align stage. ThevW/vA/vGattribute flags also collided with the recently-landedGX/GN/nM(NMM) flags; WASP tags were moved to bits 12–14.Validation (vs STAR 2.7.11b, 10k yeast SE + a 60-SNV het VCF over covered loci)
vWdistribution byte-exact: rustar and STAR both236 × vW:i:1,59 × vW:i:2,9 × vW:i:6.vW:2for its own mapping; not a WASP-logic difference.--waspOutputMode SAMtag).test_wasp_samtagintegration test (synthetic genome + planted het SNV → all 10 unique overlapping reads getvW:i:1).Gate: 569 tests pass ·
clippy --all-targets0 warnings ·fmtclean.Note: STAR requires
--outSAMtype BAMwith--waspOutputMode; rustar also accepts SAM output.