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gtars-core

Core library providing fundamental data structures and utilities for genomic interval operations. This is the foundation that all other gtars modules build upon.

Features

  • Common genomic data structures (Region, RegionSet)
  • BED file parsing utilities
  • Shared constants and helper functions
  • Foundation for all gtars modules

Core Data Types

Region

Represents a genomic interval with chromosome, start, and end coordinates: 

use gtars_core::models::Region;

// Create a region
let region = Region::new("chr1", 1000, 2000);

// Access properties
println!("Chr: {}", region.chr);
println!("Start: {}", region.start);
println!("End: {}", region.end);

RegionSet

Collection of genomic regions: 

use gtars_core::models::RegionSet;
use std::path::Path;

// Load from BED file
let rs = RegionSet::try_from(Path::new("peaks.bed"))?;

// Access regions
println!("Number of regions: {}", rs.regions.len());

// Iterate over regions
for region in &rs.regions {
    println!("{}: {}-{}", region.chr, region.start, region.end);
}

Available Modules

  • models - Core data structures (Region, RegionSet)
  • utils - Utility functions for file handling and parsing
  • consts - Shared constants

Dependencies

Minimal external dependencies:

  • anyhow - Error handling
  • flate2 - Gzip compression support
  • Other standard bioinformatics libraries

This module serves as the foundation for all other gtars modules and maintains backward compatibility within major versions.