Release as a Rust library, too

[ewels]

Look into making functionality available as a Rust library, as well as a CLI.

https://bsky.app/profile/nickminor.bsky.social/post/3mik7x4vrlk2d

[ewels]

Feasibility Analysis: Library Crate

Investigated the current architecture to assess how much work this would be. Verdict: feasible with moderate effort. The codebase is already well-structured for it.

What's already good

• QC modules are UI-free: All terminal output (ui. calls) is confined to main.rs. The core modules (rna/, gtf, config, io) have zero UI dependencies.
• Clean sub-module APIs: dupradar, featurecounts, qualimap, rseqc, and preseq already have public functions and types that could be used independently.
• Semver-friendly timing: At 0.1.1, breaking changes are fine under semver.

What needs changing

1. Move Strandedness out of cli.rs: This enum is used by 6 non-CLI modules (config, dupradar/counting, qualimap/accumulator, qualimap/output, qualimap/report, rseqc/infer_experiment). It needs to live in a shared location rather than the CLI module.
2. Create src/lib.rs with public re-exports of the core modules, and add a [lib] section to Cargo.toml alongside the existing [[bin]].
3. Update main.rs to consume the library (use rustqc::*) instead of declaring modules directly.

Considerations

• C++ build dependency: The cpp_rng module compiles C++ via build.rs for preseq compatibility. Library consumers inherit this. Could be made optional via a feature flag.
• Heavy dependencies: rust-htslib (static), plotters, etc. Feature flags could let users opt out of plotting.
• Pipeline orchestration: The 1700-line run_rna() interleaves core logic with UI output. For an initial library release, exposing individual tool modules is sufficient without extracting a library-level pipeline runner. That can come later based on demand.
• API stability: Should start with a minimal public surface and expand based on user needs.

Rough effort estimate

Task	Effort
Move Strandedness, create lib.rs, update Cargo.toml	Small
Update main.rs to use library imports	Small
Audit and add pub visibility where needed	Small-Medium
Optional: feature flags for plotting/preseq	Medium
Optional: extract pipeline orchestration from run_rna()	Large

The minimal viable library (first three rows) is straightforward. The optional items can be done incrementally.