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[noamteyssier]

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[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 primarily focuses on expanding the bqtools encoding capabilities to efficiently handle multiple input files, including collation into a single output. It involves a substantial refactoring of the encoding command's internal structure for better modularity and introduces new CLI options for improved user experience. Additionally, it includes dependency updates and minor quality-of-life improvements across the codebase.

Highlights

• Multi-file Encoding and Collation: Introduced the ability to encode multiple FASTX files into a single BINSEQ file, supporting both single and paired-end inputs. This is managed via new --collate and --paired flags, enhancing bqtools's capability to handle large datasets more flexibly.
• Encoding Logic Refactoring: The core encoding functions have been significantly refactored and moved into a new src/commands/encode/encode.rs module. This centralizes the encoding process for various collection types and output modes, improving code organization and maintainability.
• Dependency Updates: The bqtools version has been updated to 0.4.15, and the paraseq dependency has been upgraded to 0.4.7, bringing in the latest features and fixes from the underlying parallel sequencing library.
• Improved Input Handling: The CLI now supports an unbounded number of input files for encoding, allowing for more flexible batch processing. New methods like build_single_collection, build_paired_collection, and build_interleaved_collection were added to handle these diverse input scenarios.
• Enhanced Documentation: The README.md has been updated with a new section detailing how to encode multiple files simultaneously, including practical examples for collating various FASTX inputs into BINSEQ.

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Code Review

This pull request introduces a significant refactoring of the encode command to support encoding multiple files, including recursive directory traversal, manifest files, and collating multiple inputs into a single output. The changes are well-structured, removing a lot of duplicated code and making the logic easier to follow.

I've left a couple of comments with suggestions for improvement: one to handle a potential panic on non-UTF8 file paths, and another to further reduce code duplication in the CLI input handling.

Overall, this is a great enhancement to the tool's capabilities and code quality.