gtars-overlaprs

Core infrastructure for all genomic interval overlap computations.

Purpose

gtars-overlaprs provides the foundational overlap computation primitives that all other modules build upon. This is the single source of truth for efficient interval operations in gtars.

Features

• Efficient interval intersection algorithms using AIList data structure
• Coverage calculations with bit vectors
• Support for large-scale genomic datasets (millions of intervals)
• Optimized memory usage and logarithmic query time
• Common Overlapper trait for consistent interface

Usage

From Rust

use gtars_overlaprs::{AIList, Interval};

// Create an AIList from intervals
let mut ailist = AIList::new();
ailist.add(Interval::new(100, 200));
ailist.add(Interval::new(150, 250));

// Query overlaps
let overlaps = ailist.query(120, 180);

Data Structures

• AIList - Augmented Interval List for fast overlap queries
• Bits - Bit vector implementation for coverage calculations
• Overlapper - Trait for implementing overlap operations

Performance

Optimized for:

• Large BED files (millions of intervals)
• Fast overlap queries (logarithmic time)
• Memory efficiency through compact data structures