iimpulse / rsvart

A re-implementation of svart in rust.

rsvart

A re-implementation of svart in rust. Svart is a small library for representing genomic variants and regions. It attempts to solve several common issues:

• Coordinate system off-by-one errors
• Representation of VCF small, structural and breakend variants with a consistent API
• Different variant trimming strategies
• The library provides a consistent API for creating, manipulating and comparing variation of different types by providing default
• implementations and extensible base classes and interfaces along with immutable default implementations which developers can utilise to gain maximum utility from a minimum amount of code without having to address issues in bioinformatics which are a common source of duplicated code and frequently errors.

The code is completely free of external dependencies.

Motivation

This is intended to be used as a standard library for bioinformatics in rust. Its motivation is a way for us to become rustaceans.

Development

Testing

cargo test

Building

cargo build

rsvart's Issues

creating reusable custom error in rust

implement contig from svart

Update Contig

We want to update contig and pull out enums.

implement strand from svart

Change integral data types in `Contig`

Let's use u16 for contig ID and u32 for contig length.

discuss the auto dereferencing when calling method

Implement `Region`

Let's implement Svart's Region trait.

First come, first served!