Crate recmap

Functionality for reading and working with recombination maps.

RecMap objects can be created from reading in a HapMap-formatted recombination map. Note that since the HapMap recombination format does not include the chromosome lengths, this must be specified too. A convenience function read_seqlens is provided to read in TSV-formatted “genome” files of the chromosome names and lengths.

Here is a example which loads a recombination map from a HapMap-formatted recombination map and calculates the total map lengths.

use recmap::prelude::*;
let seqlens = read_seqlens("hg38_seqlens.tsv")
                  .expect("could not read seqlens");
let rec_map = RecMap::from_hapmap("decode_2019_map.txt", seqlens)
                  .expect("cannot read hapmap");

for (name, rate_map) in rec_map.iter() {
    println!("{}\t{}", name, rate_map.total_map_length().unwrap());
}

This example can be run on the command line with:

cargo run --example  calc_map_lengths --  --seqlens hg38_seqlens.tsv decode_2019_map.txt

use recmap::prelude::*;
let seqlens = read_seqlens("hg38_seqlens.tsv")
                  .expect("could not read seqlens");
let rec_map = RecMap::from_hapmap("decode_2019_map.txt", seqlens)
                  .expect("cannot read hapmap");

let positions = vec![11975064, 15007450];
rec_map.interpolate_map_positions("chr1", &positions);

Re-exports

• pub use recmap::read_seqlens;
• pub use recmap::RecMap;
• pub use recmap::RecMapError;

Modules

• prelude
• recmap