fix: resolve indexing issues in traceback and bump to 0.5.1

[folded]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @folded, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses critical indexing and parameter ordering issues within the seq_smith library's core alignment and traceback logic. The changes standardize indexing to a consistent 0-based system, eliminating potential off-by-one errors and ensuring accurate calculations. A new test case has been introduced to further validate the correctness of overlapping ungapped local alignments, improving the robustness of the library. The project's version has been incremented to 0.5.1 to reflect these important fixes.

Highlights

• Indexing Correction: Resolved several indexing inconsistencies across alignment and traceback functions, ensuring consistent 0-based indexing for sequence and fragment start positions.
• Match Score Parameter Order: Corrected the parameter order for the match_score function in traceback and _top_k_ungapped_local_align_core to ensure proper scoring.
• New Test Case: Added a new test test_top_k_ungapped_overlap to validate the behavior of overlapping ungapped local alignments, enhancing test coverage.
• Version Bump: Updated the project version to 0.5.1 across Cargo.toml, pyproject.toml, and uv.lock.

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[gemini-code-assist]

Code Review

This pull request primarily focuses on fixing several indexing-related bugs within the alignment logic, particularly in the traceback and _top_k_ungapped_local_align_core functions. The changes correctly resolve issues with 1-based versus 0-based indexing and incorrect argument passing to scoring functions. The version bump to 0.5.1 is consistent with these fixes. The updates to the test suite, including a new test for overlapping alignments, are valuable additions that improve test coverage. My review includes a couple of suggestions to enhance performance by eliminating redundant array lookups in performance-sensitive loops. Overall, this is a solid set of fixes that improves the correctness and robustness of the library.

[gemini-code-assist]

This block can be made more efficient. The residues are fetched for the equality check, and then fetched again inside params.match_score. You can fetch them once and reuse the values to directly access the score matrix, avoiding the overhead of the match_score method call and redundant lookups within this hot loop.

                    let residue_a = params.sa[c];
                    let residue_b = params.sb[r];
                    if residue_a == residue_b {
                        stats.num_exact_matches += 1;
                    } else {
                        let score = params.score_matrix[[residue_a as usize, residue_b as usize]];
                        if score > 0 {
                            stats.num_positive_mismatches += 1;
                        } else {
                            stats.num_negative_mismatches += 1;
                        }
                    }