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feat(io): detect input compression by magic bytes, optional bz2/zstd/xz - #272
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FASTQ input is now identified by content instead of extension. gzip is always decoded with MultiGzDecoder; bzip2, zstd and xz are optional pure-Rust features (bz2, zstd, xz, compressed-input). A detected format whose feature is not built fails with an error naming the feature and a --readFilesCommand alternative. Closes #218 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Closes #218.
--readFilesCommandstill takes precedence.MultiGzDecoder(multi-member input is read in full).bz2(bzip2 0.6),zstd(ruzstd 0.9, with a multi-frame adapter),xz(lzma-rust2 0.21), andcompressed-inputfor all three. Default features are unchanged.--readFilesCommandalternative.Behaviour change to review: a plain file named
*.gzis now read as plain text, and gzip is decoded whatever the filename. Documented in DIVERGENCE.md §4.3. TheParameters_openReadsFiles.cppcitation there should be double-checked.Conflicts expected: #219 (same
MultiGzDecoderchange infastq.rs), #225 (rapidgzip would move into theGziparm ofcompression.rs; both add[features]).Tests: fmt, clippy 0 warnings,
cargo testwith default and all features. Test data is generated at runtime.🤖 Generated with Claude Code