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feat(solo): optional CellRanger v3 .h5 count matrices via hdf5-pure - #275
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BenjaminDEMAILLE wants to merge 2 commits into
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New hdf5-out feature (pure-Rust hdf5-pure) and --soloOutH5 yes|no (default no). Writes raw_feature_bc_matrix.h5 and, when present, filtered_feature_bc_matrix.h5 per Gene/GeneFull feature, converted from the MatrixMarket output. CI lints and tests the feature. Refs #270 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Cargo.toml: main's noodles-bgzf 0.51 plus this branch's optional hdf5-pure and its feature. tests/alignment_features.rs: main's file with this branch's soloOutH5 tests re-added. src/solo/h5.rs: assert_eq! on the empty dataset, for clippy's assert_is_empty lint. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Refs #270 (the issue is "for consideration"; this is a concrete, conservative proposal).
hdf5-outfeature (hdf5-pure0.47, pure Rust, MIT/Apache-2.0). Default build unchanged.--soloOutH5 yes|no(defaultno);yeswithout the feature errors clearly.raw_feature_bc_matrix.h5and, when present,filtered_feature_bc_matrix.h5per Gene/GeneFull feature (SmartSeq: Gene), in CellRanger v3 layout. Verified with h5py/h5ls.src/solo/count.rsis untouched and counts equal the.mtx. Only a trivial conflict with feat: outputanndata#237 expected insrc/lib.rs.features/genomeis empty.Open questions: is there a consumer for
.h5(scanpy/Seurat/CellBender read the MTX directory), and should this become a--soloOutputFormatvalue once #237 lands?Tests: fmt, clippy 0 warnings with and without features,
cargo testboth ways, 5 unit + 3 integration tests.🤖 Generated with Claude Code