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salmon_core/
lib.rs

1//! `salmon-core`: shared foundational types for the Rust port of salmon.
2//!
3//! This crate holds the vocabulary types used across the mapping, alignment,
4//! modeling, and inference crates: library formats, mate status, the
5//! [`Transcript`] record with its concurrent count/mass state, log-space math
6//! helpers, and the shared error type. It deliberately has no heavy
7//! dependencies so every other crate can depend on it cheaply.
8
9pub mod atomic;
10pub mod error;
11pub mod genemap;
12pub mod libtype;
13pub mod mate;
14pub mod math;
15pub mod progress;
16pub mod quantmerge;
17pub mod refprovider;
18pub mod transcript;
19
20pub use atomic::AtomicF64;
21pub use libtype::{compatible_paired, compatible_single, is_compatible};
22pub use progress::ProgressCounters;
23pub use refprovider::RefProvider;
24
25pub use error::{Result, SalmonError};
26pub use libtype::{LibraryFormat, ReadOrientation, ReadStrandedness, ReadType};
27pub use mate::MateStatus;
28pub use transcript::Transcript;