Merge branch 'main' into pr/pinin4fjords/45

Author: flying-sheep

.github/workflows/ci.yml

@@ -94,7 +94,7 @@ jobs:
 
       - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # ratchet:Swatinem/rust-cache@v2.9.1
 
-      - run: cargo clippy -- -D warnings
+      - run: cargo clippy --all-targets -- -D warnings
 
   msrv:
     name: MSRV check

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+	"rust-analyzer.check.command": "clippy",
+	"[rust]": {
+		"editor.formatOnSave": true,
+		"editor.defaultFormatter": "rust-lang.rust-analyzer"
+	}
+}

CLAUDE.md

@@ -20,15 +20,15 @@ The primary goal is a faithful port — matching the original STAR behavior as c
 Rust 2024 edition. Standard Cargo commands:
 
 ```bash
-cargo build            # Debug build
-cargo build --release  # Release build
-cargo test             # Run all tests
-cargo test <name>      # Run a single test by name
-cargo clippy           # Lint
-cargo fmt              # Format code
+cargo build                 # Debug build
+cargo build --release       # Release build
+cargo test                  # Run all tests
+cargo test <name>           # Run a single test by name
+cargo clippy --all-targets  # Lint
+cargo fmt                   # Format code
 ```
 
-Always run `cargo clippy`, `cargo fmt --check`, and `cargo test` before considering a phase complete.
+Always run `cargo clippy --all-targets`, `cargo fmt --check`, and `cargo test` before considering a phase complete.
 
 ## Current Status
 

CONTRIBUTING.md

@@ -5,11 +5,11 @@
 Rust 2024 edition. Standard Cargo commands:
 
 ```bash
-cargo build            # debug build
-cargo build --release  # release build
-cargo test             # run all tests
-cargo clippy           # lint (zero warnings expected)
-cargo fmt --check      # formatting check
+cargo build                 # debug build
+cargo build --release       # release build
+cargo test                  # run all tests
+cargo clippy --all-targets  # lint (zero warnings expected)
+cargo fmt --check           # formatting check
 ```
 
 CI runs on Linux (x86_64, x86-64-v3, aarch64), macOS (aarch64), and Windows (x86_64). PRs must pass all CI checks before merging.

README.md

@@ -155,10 +155,10 @@ See [ROADMAP.md](ROADMAP.md) for detailed implementation tracking.
 Requires Rust 2024 edition (rustc 1.85+).
 
 ```bash
-cargo build --release    # Release build
-cargo test               # Run tests
-cargo clippy             # Lint
-cargo fmt                # Format
+cargo build --release       # Release build
+cargo test                  # Run tests
+cargo clippy --all-targets  # Lint
+cargo fmt                   # Format
 ```
 
 ## Development

docs/src/content/docs/about/contributing.md

@@ -10,11 +10,11 @@ Contributions are welcome. The repository is on GitHub at [scverse/rustar-aligne
 Rust 2024 edition. Standard Cargo commands:
 
 ```bash
-cargo build            # debug build
-cargo build --release  # release build
-cargo test             # run all tests
-cargo clippy           # lint (zero warnings expected)
-cargo fmt --check      # formatting check
+cargo build                 # debug build
+cargo build --release       # release build
+cargo test                  # run all tests
+cargo clippy --all-targets  # lint (zero warnings expected)
+cargo fmt --check           # formatting check
 ```
 
 CI runs on Linux (x86_64, x86-64-v3, aarch64), macOS (aarch64), and Windows (x86_64). PRs must pass all CI checks before merging.

docs/src/content/docs/getting-started/installation.md

@@ -87,9 +87,9 @@ target/release/rustar-aligner --version
 ### Verify the build
 
 ```bash
-cargo test            # full test suite (~396 tests)
-cargo clippy          # lint (zero warnings expected)
-cargo fmt --check     # formatting check
+cargo test                  # full test suite (~396 tests)
+cargo clippy --all-targets  # lint (zero warnings expected)
+cargo fmt --check           # formatting check
 ```
 
 ### Debug builds

src/align/mod.rs

@@ -10,4 +10,4 @@ pub use read_align::{
 };
 pub use seed::Seed;
 pub use stitch::{SeedCluster, WindowAlignment, stitch_seeds};
-pub use transcript::{CigarOp, Exon, Transcript};
+pub use transcript::{Exon, Transcript};