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v0.0.3: UMI extraction and exact deduplication - #7
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- bqc umi: six UMI locations, fastp-compatible header tagging, workflow stage - bqc dedup: exact two-pass deduplication with parallel decode/hash/encode - benchmarks vs fastp, user guide, README and changelog updated (v0.0.3)
process_chunk and Config::compile exceeded clippy's 100-line limit; the UMI extraction/clipping, result translation and stage compilation move into helpers. Behavior unchanged.
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What
The v0.0.3 feature release (version already bumped in
Cargo.toml):bqc umi— UMI extraction/relocation matching fastp--umi:read1/read2/index1/index2/per_index/per_read)--umi-prefix/--umi-delimiter), both mate names--umi-skip; short reads are an explicit error, never a truncated UMI[umi]workflowstage running before correctionbqc dedup— exact whole-dataset deduplication:--memory-mb)Plus benchmarks vs fastp
--umi/--dedup(bench.md + scripts), the userguide (usage.md:
bqc umi/5.7,bqc dedup/5.8, stage order, configexample) and README coverage.
Verification
cargo test: 363 passed (244 lib, 88 cbq, 6 dedup, 16 properties,8 umi, 1 doctest).