Crate salmon_core 

salmon-core: shared foundational types for the Rust port of salmon.

This crate holds the vocabulary types used across the mapping, alignment, modeling, and inference crates: library formats, mate status, the Transcript record with its concurrent count/mass state, log-space math helpers, and the shared error type. It deliberately has no heavy dependencies so every other crate can depend on it cheaply.

Re-exports

pub use atomic::AtomicF64;

pub use libtype::compatible_paired;

pub use libtype::compatible_single;

pub use libtype::is_compatible;

pub use progress::ProgressCounters;

pub use refprovider::RefProvider;

pub use error::Result;

pub use error::SalmonError;

pub use libtype::LibraryFormat;

pub use libtype::ReadOrientation;

pub use libtype::ReadStrandedness;

pub use libtype::ReadType;

pub use mate::MateStatus;

pub use transcript::Transcript;

Modules

atomic

Lock-free f64 accumulation, used for concurrent mass/count updates.

error

Shared error type for the salmon crates.

genemap

Transcript→gene mapping and gene-level aggregation (-g/--geneMap → quant.genes.sf), matching salmon’s aggregateEstimatesToGeneLevel.

libtype

Library format types and parsing.

mate

Mate/fragment status, mirroring pufferfish’s util::MateStatus.

math

Log-space arithmetic helpers.

progress

Shared live-progress counters for the quantification drivers.

quantmerge

salmon quantmerge: merge one column across several samples’ quant.sf (or quant.genes.sf) into a single target × sample matrix TSV.

refprovider

Access to reference sequences for alignment validation.

transcript

Transcript record: identity, lengths, accumulated mass/counts, and the effective-length computation.