Migrate BAM I/O from rust-htslib to noodles#115
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Replace rust-htslib with a pure-Rust noodles backend behind a compatibility shim at src/rna/bam/. The shim preserves the existing Reader/IndexedReader/Record API used across dupRadar, RSeQC, preseq, Qualimap, and samtools-compatible outputs. Key changes: - Add noodles-backed BAM/SAM/CRAM readers with indexed fetch support - Preserve samtools-identical CHK checksums via packed sequence bytes - Update build docs: no cmake/htslib system deps required - All integration and unit tests pass in release mode Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Replace rust-htslib build prerequisites with noodles (pure Rust) across the website docs, Dockerfile, GitHub Actions workflows, and CHANGELOG. Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
- Remove extra blank line in main.rs (cargo fmt --check) - Bump rust-version to 1.89 (required by noodles 0.111) - Update MSRV CI job to match Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
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Summary
Closes #113.
Replaces
rust-htslib(htslib C bindings) with the pure-Rust noodles crate for all BAM/SAM/CRAM I/O. A compatibility shim atsrc/rna/bam/preserves the existingReader/IndexedReader/RecordAPI so the rest of the pipeline is unchanged.Changes
src/rna/bam/module — noodles-backed readers, records, CIGAR decoding, and test fixture writer/index helpersrust-htslibremoved;noodles0.111 added withbam,sam,cram,csi,bgzf,core, andfastafeaturesg++(preseq FFI) andlibfontconfigremainAGENTS.md,CONTRIBUTING.md, andCHANGELOG.mdOutput parity
Direct A/B comparison on
tests/data/test.bam(main vs this branch) confirms bit-identical samtools outputs (flagstat,idxstats,stats), dupRadar, preseq, RSeQC text outputs, Qualimap data files, and all PNG/SVG plots. Only metadata differs (timestamps, output paths in comments, git commit hash inCITATIONS.md).Testing
CXX=g++ cargo fmt --check CXX=g++ cargo clippy -- -D warnings CXX=g++ cargo test --releaseAll unit tests and 18 integration tests pass.