feat: --peOverlapNbasesMin mate-overlap merge-and-realign#119
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BenjaminDEMAILLE wants to merge 1 commit into
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feat: --peOverlapNbasesMin mate-overlap merge-and-realign#119BenjaminDEMAILLE wants to merge 1 commit into
BenjaminDEMAILLE wants to merge 1 commit into
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Port of STAR's ReadAlign::peMergeMates / peOverlapSEtoPE (STAR-rs star_pe_overlap.rs): when mates overlap in genome space, merge them into one SE read, realign through the existing SE pipeline, and convert the result back into a two-mate pair, rescoring from scratch. Unconditional overwrite of the separate-mate result on success, per STAR semantics. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
ReadAlign::peMergeMates/peOverlapSEtoPE(sister project STAR-rsstar_pe_overlap.rs)Test plan
cargo fmt --checkcargo clippy --all-targets(0 warnings)cargo test(459 passed)