Crate biolic 

biolic: A modular bioinformatics toolkit in Rust.

biolic is designed for fast, memory-efficient processing of DNA sequencing data, with particular focus on long-read sequencing from PacBio HiFi and Oxford Nanopore.

Modules

• cli: Command-line interface definition and dispatch.
• io: File reading, writing, and format detection.
• record: The unified Record type abstracting FASTQ, FASTA, and BAM.
• modules: The actual processing modules (stats, filter, count, etc.).
• output: Output formatting (human, JSON, TSV).
• utils: Shared utility functions (quality, statistics).
• error: Error types.

Example

use biolic::io::reader::open_reader;
use biolic::record::Record;

let mut reader = open_reader("reads.fastq.gz").unwrap();
let mut total = 0;
while let Some(record) = reader.next_record().unwrap() {
    total += record.seq.len();
}
println!("Total bases: {}", total);

Re-exports

pub use error::BiolicError;

pub use record::Record;

Modules

cli

Top-level CLI definition.

error

Error types for biolic.

io

Input/output abstractions.

modules

Module dispatch.

output

Output formatting (human-readable, JSON, TSV).

record

The unified Record type.

utils

Shared utility functions.