fix(align): pair-subset dedup requires same chromosome and strand (stacked on #254) - #271
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…nd strand STAR runs blocksOverlap inside a single window, so both transcripts always share chromosome and strand. Require the same in dedup_pair_subsets so a diagonal coincidence across strands or chromosomes can never count as a subset. Adds tests for the strand guard and blocksOverlap diagonal logic. Refs #31 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Stacked on #254. STAR's
blocksOverlaponly ever compares transcripts inside one window, so both share chromosome and strand.dedup_pair_subsetsnow requires the same, so a diagonal coincidence across strands or chromosomes can't count as a subset.Adds two unit tests: the strand guard, and the
blocksOverlapdiagonal logic.Not re-benchmarked on the #31 fixture (not available locally). The guard should leave #254's numbers unchanged, but that is not verified.
Refs #31
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