Ben consolidation 1 - #134
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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>
# Conflicts: # Cargo.lock
…oid) Port STAR-rs's genomeGenerate-time genome transform from STAR-rs `crates/star-index/src/transform.rs` (itself a port of STAR's `Genome_transformGenome.cpp`): substitute a VCF's alleles into the reference genome before the suffix array is built, so reads carrying the alternate allele map with fewer mismatches. Scoped to Haploid only (Diploid — duplicating the genome into `_h1`/`_h2` haplotypes — is a follow-up), and to genomeGenerate only: with the only supported `--genomeTransformOutput` (`None`, STAR's own default), the aligner reports transformed-genome coordinates directly, so align-time back-transform isn't needed and isn't implemented. `Parameters::validate` loudly rejects Diploid, an unknown transform type, a missing VCF, or combining a transform with a GTF (STAR itself doesn't support that combination either). - src/genome/transform.rs: parse_vcf_haploid (first ALT allele per record, no genotype filtering, STAR's overlap filter), transform_one_chromosome (per-chromosome allele substitution in chromosome-local coordinates; indels shift length and split the block map), transform_chromosomes (globalizes blocks using compute_chr_starts run once over original lengths and once over transformed lengths), blocks_to_tsv (transformGenomeBlocks.tsv, STAR's reverse-conversion format). - src/genome/mod.rs: extract compute_chr_starts (STAR's bin-padding formula) out of Genome::from_fasta as a shared helper; hook the transform in from_fasta right after FASTA parsing (indel-resized chromosomes flow unchanged through the existing padding/RC-buffer logic below); add Genome::transform_blocks, written to transformGenomeBlocks.tsv by write_index_files when present. - src/lib.rs: genome_generate() also writes the untransformed index to `<genomeDir>/OriginalGenome/` (STAR's own layout) by re-running generate_streaming with the transform disabled and the output directory redirected. - src/params/mod.rs: --genomeTransformType (None/Haploid), --genomeTransformVCF. Adding the `transform_blocks` field to `Genome` required threading `None` through ~28 existing test-only struct literals across align/chimeric/io/ junction/quant/signal (mechanical, no behavior change). Verified end-to-end on a tiny fixture beyond the unit tests: genomeGenerate with --genomeTransformType Haploid produces a transformed Genome file with the VCF allele substituted at the right offset, an untouched OriginalGenome/, and a transformGenomeBlocks.tsv with the correct identity block; the three validation rejections (missing VCF, Diploid, unknown type) all fire correctly. Gate green: cargo build --all-targets, clippy -D warnings, fmt, 478 tests (4 new transform 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>
…oid) Genotype-aware transform ported from STAR-rs: parse_vcf_diploid reads the sample GT field per haplotype, transform_genome_diploid runs the Haploid substitution once per haplotype and concatenates chr_h1/chr_h2 with new_start offset by hap0's padded genome length. Rejects Diploid at validate() time no longer; both Haploid and Diploid now share the same genomeGenerate path, writing one OriginalGenome/ for both haplotypes. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Parses chr/start/end/[strand] TSV files (1-based intron first/last base) into the same raw junction shape produced by GTF parsing, and unions them with any --sjdbGTFfile junctions before sjdb insertion into the genome/SA. Works standalone (no GTF): junction_db and the sjdb files are built whenever the union is non-empty; only the transcriptome index requires a GTF. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Makes the GTF attribute keys for gene name/biotype configurable (multi-candidate, last-match-in-list wins, matching STAR's find_attr_list), and fixes a latent gap where the hardcoded lookup only ever checked gene_biotype: GENCODE-style GTFs using gene_type fell back to the literal "MissingGeneType" even though STAR's default candidate list (gene_type, gene_biotype) would have picked it up. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Ports STAR's bamRemoveDuplicates (STAR-rs star-io/bam.rs): marks PCR duplicates in a coordinate-sorted BAM by grouping reads into maximal overlapping clusters, pairing unique mappers by name, and keeping only the highest-AS pair per (start, flag, S-extended CIGAR) key. NH/AS tags are required. Writes <prefix>Processed.out.bam. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…d records) Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Threads a configurable HI-tag start value through all SAM/BAM record writers (SE multimapper, PE mate records, transcriptome projection, half-mapped fallback): default 1 matches STAR; 0 matches the CellRanger convention. The secondary FLAG bit stays rank-based and is unaffected by the shift. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds the missing RunMode::LiftOver variant (a prior stub referenced it without defining it, so this run mode never compiled) and ports STAR's Chain::chainLoad / Chain::liftOverGTF (STAR-rs chain.rs) to lift --sjdbGTFfile coordinates through the first --genomeChainFiles chain file. Writes <prefix>GTFliftOver_1.gtf plus a .unlifted sidecar for features that fall in an unaligned gap. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Psy-Fer
enabled auto-merge (squash)
July 25, 2026 07:31
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This PR consolidates a number of PRs from @BenjaminDEMAILLE
Each was tested, and fixed where there were issues.
It closes #106 #115 #117 #120 #121 #126 #127 #128