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Superseded by the consolidated seqtree 1.1.0 release PR #13; its implementation and validation are retained there.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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Total junction-plus-gene distances need the same nonnegative group offsets on matrix, ball and count paths. Add optional group IDs and an offset matrix to the existing batched gap-block APIs, preserving sequence-only defaults and full-sequence identity exclusion.
Validation: 178 focused checks, unchanged default numerical hashes, independent review and boundary validation. Stacked on the positional-scoring feature.