gtarslisted

# Gtars: Genomic Tools and Algorithms in Rust ## Overview Gtars is a high-performance Rust toolkit for manipulating, analyzing, and processing genomic interval data. It provides specialized tools for overlap detection, coverage analysis, tokenization for machine learning, and reference sequence management. Use this skill when working with: - Genomic interval files (BED format) - Overlap detection between genomic regions - Coverage track generation (WIG, BigWig) - Genomic ML preprocessing and tokenization - Fragment analysis in single-cell genomics - Reference sequence retrieval and validation ## Installation ### Python Installation Install gtars Python bindings: ```bash uv uv pip install gtars ``` ### CLI Installation Install command-line tools (requires Rust/Cargo): ```bash # Install with all features cargo install gtars-cli --features "uniwig overlaprs igd bbcache scoring fragsplit" # Or install specific features only cargo install gtars-cli --features "uniwig overlaprs" ``` ### Rust Library Add to Cargo.toml for Rust projects: ```toml [dependencies] gtars = { version = "0.1", features = ["tokenizers", "overlaprs"] } ``` ## Core Capabilities Gtars is organized into specialized modules, each focused on specific genomic analysis tasks: ### 1. Overlap Detection and IGD Indexing Efficiently detect overlaps between genomic intervals using the Integrated Genome Database (IGD) data structure. **When to use:** - Finding overlapping regulatory elements - Variant a