A PAF file parser

Simple iterator API for PAF files.

Example

Run this example with cargo run --release --examples ./data/5_GD_domestica.paf. The data is in this repository.

use paf::Reader;
use std::env;

fn main() {
    let data = env::args().skip(1).next();

    if let Some(filename) = data {
        let mut reader = Reader::from_path(&filename).unwrap();
        for record in reader.records() {
            let record = record.unwrap();
            println!("{:?}", record);
        }
    } else {
        eprintln!("Usage: cargo run --release --examples print_paf <filename>");
        std::process::exit(1);
    }
}

lib.rs:

The paf crate parses PAF files. PAF is a Pairwise mApping Format which is commonly used to represent the mapping between two sets of sequences. This crate is based on output produced from minimap2, so please see the documentation of minimap2 to see the full set of fields that can be present in a PAF file.

Example

use paf::Reader;
use std::env;

fn main() {
let data = env::args().skip(1).next();

if let Some(filename) = data {
let mut reader = Reader::from_path(&filename).unwrap();
for record in reader.records() {
let record = record.unwrap();
println!("{:?}", record);
}
} else {
eprintln!("Usage: print_paf <filename>");
std::process::exit(1);
}
}