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feat(io): optional paraseq FASTQ backend - #273
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Adds paraseq 0.6 behind the paraseq feature, selected at runtime with RUSTAR_FASTQ_BACKEND=paraseq. Record encoding is shared with the noodles path so both produce identical reads; equivalence tests cover SE, PE, gzip, CRLF and non-default quality parameters. Closes #95 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Closes #95 ("praseq" is
paraseq0.6 on crates.io).paraseqfeature, off by default. When built with it,RUSTAR_FASTQ_BACKEND=paraseqswitches the reader at run time (same pattern as feat(io): optional pure-Rust parallel gzip input decoding (rapidgzip-core) #225's env gate).Reader-only throughput, 1M x 150 bp: plain 0.42 s → 0.26 s (~1.6x), gzip-1 0.52 s → 0.36 s (~1.45x). The aligner consumes far less than either, so end-to-end gain is expected to be small.
Tests: 6 equivalence tests (SE, PE, gzip, CRLF, non-default quality params, uneven PE, truncation).
cargo testpasses with and without the feature, clippy 0 warnings.Note: overlaps #218 in the gzip branch of
fastq.rs; after #218 lands, paraseq should read from itsopen_decoded.🤖 Generated with Claude Code