Short usage doesn't match full help

If I give no inputs, the short help appears as expected, but it seems to be missing some of the options that appear in the full help (-r, --ref-fasta for example)

$ perbase base-depth
error: The following required arguments were not provided:

USAGE:
    perbase-linux-amd64 base-depth <reads> --channel-size-modifier <channel-size-modifier> --chunksize <chunksize> --compression-level <compression-level> --compression-threads <compression-threads> --exclude-flags <exclude-flags> --include-flags <include-flags> --mate-resolution-strategy <mate-resolution-strategy> --max-depth <max-depth> --min-mapq <min-mapq> --ref-cache-size <ref-cache-size> --threads <threads>

If this common is a common convention, feel free to ignore, but it surprised me when looking for the fasta argument

See fixes in 76e38e6

Running subcommands with no args will now print the full help, instead of the oddly shortened help that wasn't including all options as you noted.

Thanks for the suggestions, feel free to re-open if needed!

@chrisamiller

@chrisamiller - I've had to roll back this change due to #104.

Just wanted to let you know in case it changes any evaluation! I don't think there's a way to get the sort of help message your describing at this time. I probably need to switch to clap over structopt and will leave this open as an enhancement.

Navigation Menu

Repository navigation

Short usage doesn't match full help #101

Metadata

Assignees

Labels

Projects

Milestone

Relationships

Development

Short usage doesn't match full help #101

Description

Activity

sstadick commented on Feb 3, 2026

sstadick commented on Feb 4, 2026

Metadata

Metadata

Assignees

Labels

Projects

Milestone

Relationships

Development

Issue actions