Crate rsomics_bam_junctions 

Annotate splice junctions from spliced BAM reads against a BED12 gene model.

Mirrors RSeQC junction_annotation.py (LGPL-2.1+):

• extracts every N-op intron from each read’s CIGAR string;
• filters by minimum intron length and MAPQ;
• classifies each (chrom, intron_start, intron_end) as known (both splice sites present in the BED12 intron set), partial_novel (one site known), or complete_novel (neither site known);
• counts both per-read events and distinct junctions.

Origin

This crate is an independent Rust reimplementation based on:

• RSeQC: junction_annotation.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

No source code from the GPL/LGPL upstream was used as reference during implementation; the algorithm is derived from the published method, the public format specs, and black-box behavioural testing.

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

Structs

JunctionCounts

Summary counts produced by junction annotation.

KnownSites

Known splice-site sets built from the BED12 intron boundaries.

Enums

JunctionClass

Classification of a splice junction relative to the gene model.

Functions

annotate_junctions

Annotate splice junctions from bam_path against the BED12 gene model at bed_path.