salmon_model/
lib.rs

1//! `salmon-model`: statistical models used during quantification.
2//!
3//! Currently provides the fragment-length distribution ([`fld`]) and automatic
4//! library-type detection ([`libdetect`]). Bias models (sequence-specific, GC,
5//! positional) and the alignment error model are added in later phases.
6
7pub mod bias;
8pub mod dumps;
9pub mod fld;
10pub mod gcbias;
11pub mod libdetect;
12pub mod posbias;
13pub mod seqbias;
14pub mod spline;
15
16pub use bias::{
17    build_expected_pos, corrected_effective_length_full, positional_factor, BiasInputs,
18};
19pub use fld::{ambig_frag_log_prob, smoothed_effective_length, FragmentLengthDistribution};
20pub use gcbias::{
21    build_expected_gc, gc_corrected_effective_length, gc_desc, gc_prefix, gc_ratio, GcFragModel,
22    GcRank, GcStore, GcView, GC_SAMP_STRIDE,
23};
24pub use libdetect::LibraryTypeDetector;
25pub use posbias::{
26    compute_length_quantiles, length_class_index, SimplePosBias, NUM_LENGTH_CLASSES, NUM_POS_BINS,
27};
28pub use seqbias::{build_expected, corrected_effective_length, SBModel};
salmon_model/lib.rs

salmon_model/
lib.rs
