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docs: correct the FASTQ shuffling page (#870) - #871
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The page claimed seqkit shuffle streams from disk with bounded memory; it reads every record into memory. Its paired example passed both mates with -2, which is --two-pass (FASTA only), not a paired mode, and would shuffle the mates together into one output. Shuffle each mate separately with the same seed instead; seqkit's permutation depends only on the seed and the record count. Also say why order matters (aligner batches) and point to #870. Co-Authored-By: Claude <noreply@anthropic.com>
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Refs #870.
docs-site/src/gen-reads/fastq-shuffling.mdhad two errors, each checked against seqkit's own usage text and source:shuffle.goappends every record to a slice before shuffling.seqkit shuffle -2 R1 R2 -o … -o …uses-2, which is--two-passand FASTA only, not a paired mode. Both inputs would be read as one stream and shuffled together.The fix: shuffle each mate separately with the same
-s.shuffle.goseeds one generator from-sand callsr.Shuffle(len(sequences), …), so the permutation depends only on the seed and the record count. That is from reading the source; I have not run seqkit.germline_e2e.sbatchalready shuffles this way, underSHUFFLE=1.The page also now says why order matters (aligner batches; variant calling does not depend on it) and points to #870.
Not verified: no seqkit run. Running seqkit's release binary here was not permitted, so the same-seed behavior rests on the source reading above.
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