57 update binseq requirement

[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 primarily focuses on upgrading the binseq dependency to version 0.7.5, along with a comprehensive update of many other project dependencies. The core logic for recoding data to BINSEQ and VBINSEQ formats has been refactored to align with the new binseq API, which now utilizes builder patterns for header creation and updated methods for writing records. Additionally, a new command-line option has been introduced to allow users to specify the bit size for BINSEQ output, enhancing flexibility.

Highlights

• Dependency Updates: The pull request includes a comprehensive update of numerous project dependencies, most notably upgrading the binseq crate from version 0.6.2 to 0.7.5.
• BINSEQ Bit Size Option: A new command-line option, --bitsize, has been introduced for the recode command, allowing users to specify the bit size (2 or 4) for BINSEQ output.
• Binseq API Adaptation: The code has been refactored to adapt to changes in the binseq crate's API, specifically moving to builder patterns for BinseqHeader and VBinseqHeader creation, and updating record writing methods.

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[gemini-code-assist]

Code Review

This pull request updates several dependencies, including a significant update to the binseq crate which introduces breaking API changes. While most of the code has been adapted correctly, I've found a critical issue in a function call that will prevent compilation, as well as a potential problem with command-line argument validation. My review includes specific suggestions to address these points.

[gemini-code-assist]

This call to write_paired_record is incorrect. It provides 7 arguments, but the function from the updated binseq crate expects 8. This will cause a compilation error. Additionally, the arguments are mismatched, leading to type errors: extended_seg.seq() is passed as a name (n2), and Some(extended_seg.qual()) is passed as a sequence (s2).

You need to pass 8 arguments, with None for the second read's name (n2), and correctly pass the sequence and quality for the second read.

Suggested change

	t_writer.write_paired_record(
	None,
	None,
	primary_seg.seq(),
	Some(primary_seg.qual()),
	None,
	extended_seg.seq(),
	primary_seg.qual(),
	extended_seg.qual(),
	Some(extended_seg.qual()),
	)?;
	t_writer.write_paired_record(
	None,
	None,
	primary_seg.seq(),
	Some(primary_seg.qual()),
	None,
	None,
	extended_seg.seq(),
	Some(extended_seg.qual()),
	)?;

[gemini-code-assist]

The current implementation of bitsize() silently treats any value other than 4 as 2. This could lead to unexpected behavior if a user provides an invalid value like 3. It's better to validate the input and fail fast by panicking for unsupported values.

An even better approach would be to use clap's validation capabilities to reject invalid values at the argument parsing stage, for example by using value_parser.

    pub fn bitsize(&self) -> BitSize {
        match self.bitsize {
            2 => BitSize::Two,
            4 => BitSize::Four,
            other => panic!(
                "Invalid bitsize: {}. Only 2 or 4 are supported.", other
            ),
        }
    }