Crate rsomics_bam_strandedness 

Infer RNA-seq library strand protocol from a BAM file and a BED12 gene model.

Mirrors the algorithm of RSeQC infer_experiment.py (LGPL):

• reads up to sample_size mapped, non-duplicate, non-secondary, non-QC-fail reads with MAPQ ≥ mapq_cut;
• for each read, finds overlapping genes in the BED12 model;
• classifies the read by (read_id, map_strand, gene_strand);
• emits forward (sp1), reverse (sp2), and undetermined fractions.

Origin

This crate is an independent Rust reimplementation based on:

• RSeQC: infer_experiment.py (LGPL-2.1+), Wang et al. 2012 https://doi.org/10.1093/bioinformatics/bts356
• The SAM/BAM format specification (MIT)
• BED12 format specification
• Black-box behaviour testing against RSeQC 5.0.4

License: MIT OR Apache-2.0. Upstream credit: RSeQC https://rseqc.sourceforge.net/ (LGPL-2.1+).

Structs

GeneIndex

Per-chromosome interval tree, mapping genomic positions → gene strands.

StrandednessResult

Result of strandedness inference.

Enums

GeneStrand

Strand of a gene (‘+’ or ‘-’).

Protocol

Whether the BAM contains paired-end or single-end reads.

Functions

infer_strandedness

Infer strandedness from bam_path using the gene model at bed_path.