libradicl

Libradicl is a Rust library for reading (and eventually writing and manipulating) Reduced Alignment Data (RAD) format files. These files are produced by salmon when preparing data for single-cell quantification with alevin-fry.

Currently, libradicl has primarily been developed in support of alevin-fry, so it has not been fully developed as as a general library quite yet. Eventually, we anticipate there will be a reorganization and a stabalization of the API.

lib.rs:

libradicl is a crate for reading (and writing) RAD (Reduced Alignment Data) format files. The RAD format is a binary format designed to encode alignment information about sequencing reads and how they map to a set of targets (a genome, metagenome, transcriptome, etc.). The format is "reduced" because it is allowed to contain sparser information than e.g. a SAM format file.

While the eventual goal of this crate is to provide a generic API to read and write RAD files that may be designed for any purpose, it is driven mostly by our (the COMBINE-lab's) needs within the tools we produce that use the RAD format (e.g. alevin-fry and piscem-infer). Thus, features are generally developed and added in the order that is most urgent to the development of these tools. However, we welcome external contributions via pull requests, and are happy to discuss your potential use cases for the RAD format, and how they might be supported.

This crate is broken into several components that cover the various parts of RAD files including the type tag system, the header, and the main data chunks. The names of each module are fairly self-explanatory.