Redesign the `fgfa` command-line interface
Nobody has claimed this yet.
- Dominant language
- Rust
- Stars
- 45
- Forks
- 3
- PR merge metrics
- No merged PRs in 30d
Description
Currently, the input and output file options are _global_ options for the `fgfa` command. So you do stuff like this:
```
fgfa -i something.flatgfa stats
```
Instead of:
```
fgfa stats -i something.flatgfa
```
Or even:
```
fgfa stats something.flatgfa
```
As a purely cosmetic thing like that, this wouldn't be worth worrying about. But it actually causes a bunch of annoyance for the growing number of commands that _don't_ read and/or write a variation graph. All these special cases are just to ignore the GFA/FlatGFA input arguments, for example, in cases where we don't need it:
https://github.com/cucapra/pollen/blob/c243c6f69aefb48ca77d47f1991c326b1f460827/flatgfa/src/cli/main.rs#L67-L84
Let's redesign the CLI so the input and output flags are per-subcommand.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading flatgfa/src/cli/main.rs, especially lines 67-84 referenced in the issue, and trace the CLI entry points for its subcommands. Redesign the command interface so input and output options belong to relevant subcommands, then verify the example stats invocations work without forcing unrelated commands to handle GFA/FlatGFA arguments.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- rust
- Domain
- cli
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100