Clarify --fixed-crop help text

[JMencius]

I noticed a small documentation error in README.md while using chopper v0.14.0.

When using --trim-approach fixed-crop, only one of --headcrop or --tailcrop needs to be greater than 0; they are not both required.

This matches the validation logic in src/main.rs (lines 248–253):

if args.headcrop == 0 && args.tailcrop == 0 {
    eprintln!(
        "Error: When using the 'fixed-crop' trimming approach, at least one of --headcrop or --tailcrop must be greater than 0."
    );
    std::process::exit(1);
}

A minimal test using only --headcrop also confirms this behavior:

$ printf '@test\nACGTACGT\n+\nIIIIIIII\n' |
    chopper --trim-approach fixed-crop --headcrop 2

@test
GTACGT
+
IIIIII
Kept 1 reads out of 1 reads

[wdecoster]

Thanks @JMencius — good catch, and thanks for digging up the validation code and a reproducer along with it. You were exactly right: only one of --headcrop/--tailcrop has to be non-zero.

The README options block is a paste of chopper --help, so I pushed a follow-up commit to your branch applying the same correction to the FixedCrop doc comment in src/main.rs that the help text is generated from — otherwise chopper --help would keep printing the old sentence and your fix would have been overwritten the next time the README was regenerated. I also noted on --headcrop/--tailcrop that neither is required on its own, fixed --cutoff (it is required by split-by-low-quality too, which its doc comment did not say), and regenerated the block so the README matches the binary exactly.

Merging now, and it will go out in the next release.

[JMencius]

Yeah also the source code, good fix.

…

---Original--- From: "Wouter De ***@***.***> Date: Mon, Sep 14, 2026 02:13 AM To: ***@***.***>; Cc: "Jun ***@***.******@***.***>; Subject: Re: [wdecoster/chopper] Clarify --fixed-crop help text (PR #81) Merged #81 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS and Android. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>