rsomics-coverage-core

Genome-binned BAM read-coverage primitive. Layer A library shared by rsomics-bam-signal (deeptools bamCoverage) and rsomics-bam-compare (deeptools bamCompare).

Tiles each chromosome into fixed-width bins and counts, per bin, the reads whose reference span (alignment start + reference-consuming CIGAR ops) overlaps it. Returns per-chromosome bin counts plus two read totals (total_binned for bamCoverage CPM/RPKM/RPGC, total_mapped for bamCompare's readCount scale factor).

This crate holds only the binning + counting. Normalisation, the bedGraph run-length emit, and two-BAM combination live in the consuming tool crates.

API

use std::num::NonZero;
use std::path::Path;
use rsomics_coverage_core::{compute_coverage, BinFilter};

let cov = compute_coverage(
    Path::new("in.bam"),
    50,                        // bin size (deeptools default)
    BinFilter::default(),      // accept all mapped reads
    NonZero::new(1).unwrap(),  // BGZF inflate workers
)?;
// cov.chroms: Vec<ChromBins { name, chrom_len, bins: Vec<u32> }>
// cov.total_binned, cov.total_mapped, cov.total_signal()

Origin

This crate is a Rust reimplementation of the per-bin read-counting core of deeptools (countReadsPerBin.py), informed by the deeptools source (MIT license):

• Ramírez et al., deepTools2: a next generation web server for deep-sequencing data analysis, NAR 2016. DOI: 10.1093/nar/gkw257
• deeptools source: countReadsPerBin.py, bamCoverage.py, bamCompare.py

deeptools is MIT licensed. Its source was read directly and cited here per the CONVENTIONS clean-room methodology for MIT upstreams.

License: MIT OR Apache-2.0. Upstream credit: deeptools https://github.com/deeptools/deeptools (MIT).