Crate gwseq_io 

gwseq-io

Reading and writing bigWig, bigBed, BAM and HiC files.

See ARCHITECTURE.md at the workspace root for the module map and the reasoning behind the layering.

Shape

Three readers and one writer, each opened on a path or a URL:

use gwseq_io::bbi::{ValuesRequest, Zoom};
use gwseq_io::genomic::Locs;
use gwseq_io::{open, Reader};

let chr_ids = vec!["chr1".to_string(), "chr2".to_string()];
let starts = vec![1_000_000, 2_000_000];
let ends = vec![1_010_000, 2_010_000];

let Reader::Bbi(bw) = open("track.bigwig", Default::default())? else {
    panic!("not a bigwig")
};
let values = bw.read_values(
    &ValuesRequest::new(Locs::spans(&chr_ids, &starts, &ends)?)
        .bin_size(10.0)
        .zoom(Zoom::Auto),
)?; // Array2<f32>, (loci, bins)

Requests are builders because the API they mirror has up to fourteen defaulted keyword arguments; a builder is where each default is written down once, for the Python layer, the CLI and Rust callers alike.

Threads and handles

A reader owns parallel worker threads and one file handle for its lifetime. close() gives both back and is idempotent; a closed reader fails every read with Error::Closed, while the headers it read at open stay available. A reader that is never closed gives everything back when it is dropped.

Re-exports

pub use error::Error;

pub use error::Result;

pub use genomes::get_chr_sizes;

Modules

arrays

Array shaping shared by more than one format.

bam

BAM.

bbi

bigWig and bigBed.

bytes

Little-endian field reads and writes over a byte buffer.

error

The crate’s error type.

genomes

Chromosome sizes by genome name.

genomic

Genomic coordinates: chromosome maps, loci, bins, strands.

hic

HiC contact matrices.

npz

save_to: writing a read straight to a .npz instead of through Python.

parallel

Thread pools.

progress

Progress reporting.

source

Byte sources and sinks.

Structs

OpenOptions

Everything open takes beyond the path.

Enums

FileKind

What a file’s first bytes say it is.

Reader

What open returns. The format is sniffed from the file’s magic number, not from its extension.

Functions

open

Open a file for reading, dispatching on its magic number.

sniff

Sniff the format of a file from its magic number.

sniff_source

Sniff the format of an already-open source.