## Introduction
`gtars` is a high-performance toolkit for *genomic tools and algorithms in Rust*. Built with Rust for speed and reliability, gtars provides core utilities for machine learning on genomic intervals for the [geniml](https://github.com/databio/geniml) Python package. It also provides lots of utility as a standalone library for alternative downstream use cases.
## Installation
### Rust Library
Gtars uses a feature-flag system to allow you to include only the modules you need. Add to your `Cargo.toml`:
```toml
[dependencies]
# Install specific features
gtars = { version = "0.5", features = ["overlaprs", "tokenizers"] }
# Or install from GitHub
gtars = { git = "https://github.com/databio/gtars", features = ["overlaprs", "tokenizers"] }
```
Modules:
- `core` - Core functionality and data structures
- `tokenizers` - Genomic region tokenizers
- `io` - I/O utilities
- `refget` - Reference sequence access
- `overlaprs` - Overlap operations
- `uniwig` - Coverage computation
- `igd` - Interval search
- `bbcache` - BED file caching
- `scoring` - Fragment scoring
- `fragsplit` - Fragment splitting
Example combinations:
```toml
# For machine learning tasks
gtars = { version = "0.5", features = ["tokenizers", "core"] }
# For genomic analysis
gtars = { version = "0.5", features = ["overlaprs", "uniwig", "scoring"] }
# For data access
gtars = { version = "0.5", features = ["refget", "bbcache", "io"] }
```
### Python Package
```bash
pip install gtars
```
See further documentation under Python bindings.
### Command-Line Interface
Install from source:
```bash
git clone https://github.com/databio/gtars
cd gtars
cargo install --path gtars-cli
```
Or download precompiled binaries from the [releases page](https://github.com/databio/gtars/releases).
## Development
Run tests with `cargo test` from the workspace root. Please see [CONTRIBUTING.md](https://github.com/databio/gtars/blob/master/CONTRIBUTING.md) for development guidelines.
## Module organization
`gtars` is organized into modules. The modules section gives an [overview of each module](/gtars/modules.md).
