75 incorrect decoding of extended buffer on batch decoding in bq

[noamteyssier]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @noamteyssier, 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 a critical bug related to the incorrect decoding of extended buffers during batch processing in the binseq library. The core changes involve refactoring the indexing logic within the sseq and xseq methods of the BatchRecord struct. This ensures that data is correctly sliced from the underlying buffer, especially when specific configuration flags are enabled, thereby improving the accuracy and reliability of sequence data extraction. The update also includes a minor version bump to reflect this important patch.

Highlights

• Version Update: The binseq crate version has been updated from 0.8.0 to 0.8.1, indicating a patch release.
• Decoding Logic Refactor: The sseq and xseq methods within src/bq/reader.rs have been refactored to correctly calculate buffer slice bounds.
• Incorrect Indexing Fix: This PR resolves an issue where extended buffers were incorrectly decoded during batch processing, specifically fixing indexing errors in sequence data retrieval when configuration flags are active.

Using Gemini Code Assist

The full guide for Gemini Code Assist can be found on our documentation page, here are some quick tips.

Invoking Gemini

You can request assistance from Gemini at any point by creating a comment using either /gemini <command> or @gemini-code-assist <command>. Below is a summary of the supported commands on the current page.

Feature	Command	Description
Code Review	/gemini review	Performs a code review for the current pull request in its current state.
Pull Request Summary	/gemini summary	Provides a summary of the current pull request in its current state.
Comment	@gemini-code-assist	Responds in comments when explicitly tagged, both in pull request comments and review comments.
Help	/gemini help	Displays a list of available commands.

Customization

To customize Gemini Code Assist for GitHub experience, repository maintainers can create a configuration file and/or provide a custom code review style guide (such as PEP-8 for Python) by creating and adding files to a .gemini/ folder in the base of the repository. Detailed instructions can be found here.

Limitations & Feedback

Gemini Code Assist may make mistakes. Please leave feedback on any instances where its feedback is incorrect or counter productive. You can react with 👍 and 👎 on @gemini-code-assist comments. If you're interested in giving your feedback about your experience with Gemini Code Assist for Github and other Google products, sign up here.

You can also get AI-powered code generation, chat, as well as code reviews directly in the IDE at no cost with the Gemini Code Assist IDE Extension.

Footnotes

1. Review the Privacy Notices, Generative AI Prohibited Use Policy, Terms of Service, and learn how to configure Gemini Code Assist in GitHub here. Gemini can make mistakes, so double check it and use code with caution. ↩

[gemini-code-assist]

Code Review

The pull request addresses an issue with the incorrect decoding of the extended buffer during batch processing in src/bq/reader.rs. The changes refactor the sseq and xseq methods within the BatchRecord implementation to correctly calculate the start and end bounds for the primary and extended sequences, respectively. This improves the correctness and robustness of the batch decoding logic, especially when flags are present and considering the allocated buffer sizes. The version bump in Cargo.toml is also noted.