feat: implement top-k ungapped local alignment

[folded]

• added top_k_ungapped_local_align and _many variant
• refactored AlignmentParams to remove redundant length fields
• added tests for new functionality

[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 significantly enhances the sequence alignment capabilities by introducing functionality to identify the top-k non-overlapping ungapped local alignments. This feature is crucial for applications requiring efficient discovery of multiple high-scoring regions without gaps. The implementation includes a new parameter structure tailored for ungapped alignments and is supported by parallel processing for multiple target sequences, alongside a minor refactoring of existing alignment parameter handling.

Highlights

• New Feature: Top-K Ungapped Local Alignment: Introduced top_k_ungapped_local_align and top_k_ungapped_local_align_many functions to find the highest-scoring non-overlapping ungapped local alignments (HSPs) between sequences.
• Refactored Alignment Parameters: The AlignmentParams struct was refactored to remove redundant sa_len and sb_len fields, now deriving sequence lengths directly from the sa and sb vectors.
• Dedicated Ungapped Alignment Parameters: A new UngappedAlignmentParams struct was added to specifically manage parameters for ungapped alignment calculations, ensuring clarity and separation of concerns.
• Comprehensive Testing: New test cases were added to validate the functionality of the top_k_ungapped_local_align and top_k_ungapped_local_align_many functions, covering simple cases, overlapping candidates, and the 'k' limit.

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[gemini-code-assist]

Code Review

This pull request introduces functionality for top-k ungapped local alignment, along with a parallelized _many variant. The changes also include a nice refactoring of AlignmentParams to remove redundant length fields, improving code clarity. The implementation of the new alignment algorithm is solid, using a greedy approach with a binary heap to find high-scoring pairs.

My review focuses on a few areas for improvement:

• Correctness: Ensuring consistent validation in the parallelized function.
• Maintainability: Reducing code duplication in the core alignment logic.
• Determinism: Improving the ordering of candidate alignments for more predictable results.
• Test Quality: Fixing a minor issue in the new tests.

Overall, this is a great addition to the library. The new functionality is well-implemented and the accompanying tests are thorough.

[folded]

/gemini review

[gemini-code-assist]

Code Review

This pull request introduces a significant new feature: top-k ungapped local alignment, complete with a parallelized _many variant. The implementation in Rust is robust and includes good use of data structures like BinaryHeap for efficiency. The accompanying refactoring of AlignmentParams to remove redundant length fields is a welcome improvement for code clarity and maintainability. The new functionality is also well-covered by unit tests. My review includes a few suggestions to further enhance the Rust implementation by making it more idiomatic, reducing code duplication, and refining a subtle design choice in the alignment sorting logic.