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Co-Authored-By: Codex <noreply@openai.com>
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🟡 Changes recommended
Zero-weight tables can be falsely rejected as overflowing, and the canonical API reference is incomplete.
2 open findings
What changed in this PR
Adds positional weighting and exhaustive ball reduction to native gap-block scoring.
Changes:
- Adds length-indexed positional weights to matrix and count scoring.
- Adds
ball_batchwithout dense matrix allocation. - Adds validation, documentation, and correctness tests.
| File | Description |
|---|---|
src/gapblock.cpp |
Implements weighted scoring and ball reduction. |
src/_bindings.cpp |
Exposes native APIs to Python. |
python/seqtree/gapblock.py |
Adds validation and public wrappers. |
include/seqtree/seqtree.hpp |
Declares the expanded C++ API. |
docs/gapblock.rst |
Documents weights and ball behavior. |
tests/python/test_gapblock_position_weights.py |
Tests scoring, reducers, and validation. |
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| gap_prior: GapPrior | None = None, | ||
| alphabet: str = "aa", | ||
| threads: int = 0, | ||
| position_weights_by_length=None, |
Co-Authored-By: Codex <noreply@openai.com>
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Superseded by the consolidated seqtree 1.1.0 release PR #13; its implementation and validation are retained there.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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Gap-block batch scoring currently accepts only one global substitution matrix. Add optional integer weights indexed by full sequence length, using the longer sequence as the symmetric positional frame. Equal-length scoring reduces to the original weighted substitution sum; omitted weights preserve existing behavior.
Matrix and count reducers share the same native cell. An exhaustive ball reducer returns all accepted reference rows without allocating a dense matrix. Exact exclusions, duplicate rows and reference order are preserved. Width, integer and overflow validation reject invalid tables. This does not introduce an indexed search or statistical calibration.
Validation: 121 installed-binary Python checks, 42 native oracle cells under UBSan, warning-free Sphinx build, independent review including negative-thread compatibility. Stacked on the histogram fast path; no release publication.