Fix local-global alignment initialization to allow leading gaps

[folded]

Correctly initializes the previous score row with gap costs instead of -Infinity,
permitting the global sequence (B) to start with gaps.
Adds regression test case .

[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 resolves a bug in the local-global sequence alignment algorithm that prevented it from correctly processing sequences where the global sequence (B) begins with gaps. The fix involves adjusting the initial scoring of alignment paths to properly account for gap costs, ensuring accurate alignment results for sequences with overhangs. A new regression test has been included to confirm the correct behavior of this updated logic.

Highlights

• Alignment Initialization Fix: Corrected the initialization of prev_score and hgap_score in the _local_global_align_core function to use proper gap costs instead of std::i32::MIN.
• Leading Gaps Support: This change enables the local-global alignment algorithm to correctly handle scenarios where the global sequence (B) starts with gaps.
• New Regression Test: Added a new test case, test_local_global_align_overhangs, to validate the improved handling of sequences with leading and trailing gaps in local-global alignment.
• Version Update: The seq-smith package version in uv.lock has been updated from 0.3.0 to 0.4.0.

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[gemini-code-assist]

Code Review

This pull request correctly fixes an initialization issue in the local-global alignment algorithm, allowing for alignments with leading gaps in the global sequence. The change in src/lib.rs is logical and directly addresses the problem by initializing the first column of the dynamic programming matrix with appropriate gap costs instead of negative infinity. The addition of a regression test in tests/test_seq_smith.py is excellent, as it specifically validates this fix. I've suggested a couple of improvements to the new test to make it even more robust and readable by checking all attributes of the alignment fragments.