tshauck / BioSerDe

Bioinformatics format (De)Serialization

BioSerDe

This is a PoC for the GSoC 2022 idea from GA4GH.

At present this repo just codegens .proto files borrowed from Google nucleus, but the intention is to make it SerDe friendly and eventually become a hub or "Rosetta stone" of bioinformatics format cross-conversion by leveraging Noodles as well.

Usage

% cargo run
   Compiling bioserde v0.1.0 (/Users/rvalls/dev/umccr/bioserde)
    Finished dev [unoptimized + debuginfo] target(s) in 0.28s
     Running `target/debug/bioserde`
[src/main.rs:6] create_simple_bedfile("chr1") = BedRecord {
    reference_name: "",
    start: 0,
    end: 0,
    name: "",
    score: 0.0,
    strand: NoStrand,
    thick_start: 0,
    thick_end: 0,
    item_rgb: "",
    block_count: 0,
    block_sizes: "",
    block_starts: "",
}