rsomics-bam-junctions

Annotate splice junctions from spliced BAM reads against a BED12 gene model. Rust port of RSeQC junction_annotation.py.

Usage

rsomics-bam-junctions -i <input.bam> -r <genes.bed12> [OPTIONS]

Options

Flag	Default	Description
`-i`, `--input`	required	Input BAM file
`-r`, `--refgene`	required	Reference gene model in BED12 format
`-m`, `--min-intron`	`50`	Minimum intron length (bp)
`--mapq`	`30`	Minimum MAPQ for a read to be considered
`-t`, `--threads`	auto	BGZF decompression threads
`--json`	off	Emit JSON instead of text

Output

stdout: total = N (total N-op occurrences seen, including filtered ones).

stderr: Two summary blocks separated by === lines:

Splicing events (per-read occurrences): total, known, partial novel, novel, filtered.
Splicing junctions (distinct): total, known, partial novel, novel.

Classification

Each (chrom, intron_start, intron_end) is classified against the BED12 intron set derived from consecutive exon boundaries:

known — both donor (intron start) and acceptor (intron end) are present in the BED12.
partial_novel — one site is known, the other is not.
complete_novel — neither site appears in any transcript.

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
BED12 format specification
Black-box behaviour testing against RSeQC 5.0.4

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