fix(perf): use single polars-bio overlap (no xprod) in gvl.Table#158
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Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
…gvl.Table Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Summary
Table.count_intervalsandTable._intervals_from_offsetswith a singlepb.overlap(queries, contig_subset_filtered_to_samples)call. Drops pyranges as a dependency entirely; removes the Python ≥ 3.12 /pyranges1version gate.experiments/bench_table_overlap, 5 backends × 3 sizes × 20 trials):polars_bio no_xprodis fastest at every scale (0.173 s on 2k×200×500 vs 0.422 s for the per-sample loop, 1.543 s for pyranges1 xprod) and uses ~half the memory of either pyranges variant.np.arange - np.repeat(boundaries, counts)),pl.Series.replace_strictfor sample→index mapping,np.lexsortinstead of a polars sort round-trip, hoistednumpyto module scope.Test Plan
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