alevin-fry view panicked at the prospect of providing help (or working)

[j-andrews7]

I am trying to determine what all can be done to/with the RAD file output via a typical alevin-fry quant run, but I am struggling to find much info about the view command. Ultimately, I was hoping to convert back to BAM to spotcheck induction of a mutation in our model system.

I was hoping the command line help would yield some insight, but it throws an error:

alevin-fry view -h
thread 'main' panicked at '`help`s `-h` conflicts with `header`.

To change `help`s short, call `cmd.arg(Arg::new("help")...)`.', /opt/conda/conda-bld/alevin-fry_1645548081272/work/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-3.1.1/src/build/command.rs:4249:25
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

I looked through the repo code to find the proper args (-r, etc), but it still tosses the same error and doesn't seem this subcommand is functional yet.

I'm guessing you're well aware of this, and it's uncommon for people to want to interact with the RAD files directly. But it may be a good idea to remove it from the CLI help subcommand list until it's usable.

[rob-p]

Hi @j-andrews7,

Thanks for the detailed report. Indeed, while this is not currently part of any standard workflow, there should certainly be a functional help message and there should be no panic! We'll try to clean this up for the next release.

cc @DongzeHE — do you think you could clean up the interface of the view command to avoid the conflict between header and help? One option might be to make the header flag be -H rather than -h. Also, the command should print a proper help message when -h or --help are passed.

[DongzeHE]

Hi @rob-p, yes I will do this today. Should I directly create a PR to the master branch when I am done?

[rob-p]

This is addressed in pull request #50 by @DongzeHE on develop and should be in the next release.

[rob-p]

This is now fixed in v0.5.1 — thanks again for the report!