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Superseded by the consolidated seqtree 1.1.0 release PR #13; its implementation and validation are retained there. |
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Per-input positional weights are needed when aligned sequences have different regional boundaries. The existing shared gapblock scorer now accepts query/reference weight rows and uses the larger aligned weight for each substitution, preserving symmetry for symmetric matrices. Gap costs and exact exclusion remain unchanged; length-based profiles retain their existing behavior.
The matrix, ball/count/mass and linked paired-sum APIs share this geometry, with axis/length/nonnegative/overflow validation. No domain data or confidence model is added.
Validation: exhaustive gap-layout oracle, reversed-axis symmetry, uniform-profile parity, linked reductions and 1/4-thread equality; 587 Python tests and the C++ suite pass locally, Sphinx builds without warnings. Platform CI is pending. This draft stacks on
feature/total-distance-counts; no release promotion.